| 1840 | | mso-list-template-ids:185874704 67698703 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;} |
| 1841 | | @list l11:level1 |
| 1842 | | {mso-level-tab-stop:none; |
| 1843 | | mso-level-number-position:left; |
| 1844 | | text-indent:-.25in;} |
| 1845 | | @list l11:level2 |
| 1846 | | {mso-level-tab-stop:1.0in; |
| 1847 | | mso-level-number-position:left; |
| 1848 | | text-indent:-.25in;} |
| 1849 | | @list l11:level3 |
| 1850 | | {mso-level-tab-stop:1.5in; |
| 1851 | | mso-level-number-position:left; |
| 1852 | | text-indent:-.25in;} |
| 1853 | | @list l11:level4 |
| 1854 | | {mso-level-tab-stop:2.0in; |
| 1855 | | mso-level-number-position:left; |
| 1856 | | text-indent:-.25in;} |
| 1857 | | @list l11:level5 |
| 1858 | | {mso-level-tab-stop:2.5in; |
| 1859 | | mso-level-number-position:left; |
| 1860 | | text-indent:-.25in;} |
| 1861 | | @list l11:level6 |
| 1862 | | {mso-level-tab-stop:3.0in; |
| 1863 | | mso-level-number-position:left; |
| 1864 | | text-indent:-.25in;} |
| 1865 | | @list l11:level7 |
| 1866 | | {mso-level-tab-stop:3.5in; |
| 1867 | | mso-level-number-position:left; |
| 1868 | | text-indent:-.25in;} |
| 1869 | | @list l11:level8 |
| 1870 | | {mso-level-tab-stop:4.0in; |
| 1871 | | mso-level-number-position:left; |
| 1872 | | text-indent:-.25in;} |
| 1873 | | @list l11:level9 |
| 1874 | | {mso-level-tab-stop:4.5in; |
| 1875 | | mso-level-number-position:left; |
| 1876 | | text-indent:-.25in;} |
| 1877 | | @list l12 |
| 1878 | | {mso-list-id:734669460; |
| 1879 | | mso-list-type:hybrid; |
| 1880 | | mso-list-template-ids:1988758972 67698703 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;} |
| 1881 | | @list l12:level1 |
| 1882 | | {mso-level-tab-stop:none; |
| 1883 | | mso-level-number-position:left; |
| 1884 | | text-indent:-.25in;} |
| 1885 | | @list l12:level2 |
| 1886 | | {mso-level-tab-stop:1.0in; |
| 1887 | | mso-level-number-position:left; |
| 1888 | | text-indent:-.25in;} |
| 1889 | | @list l12:level3 |
| 1890 | | {mso-level-tab-stop:1.5in; |
| 1891 | | mso-level-number-position:left; |
| 1892 | | text-indent:-.25in;} |
| 1893 | | @list l12:level4 |
| 1894 | | {mso-level-tab-stop:2.0in; |
| 1895 | | mso-level-number-position:left; |
| 1896 | | text-indent:-.25in;} |
| 1897 | | @list l12:level5 |
| 1898 | | {mso-level-tab-stop:2.5in; |
| 1899 | | mso-level-number-position:left; |
| 1900 | | text-indent:-.25in;} |
| 1901 | | @list l12:level6 |
| 1902 | | {mso-level-tab-stop:3.0in; |
| 1903 | | mso-level-number-position:left; |
| 1904 | | text-indent:-.25in;} |
| 1905 | | @list l12:level7 |
| 1906 | | {mso-level-tab-stop:3.5in; |
| 1907 | | mso-level-number-position:left; |
| 1908 | | text-indent:-.25in;} |
| 1909 | | @list l12:level8 |
| 1910 | | {mso-level-tab-stop:4.0in; |
| 1911 | | mso-level-number-position:left; |
| 1912 | | text-indent:-.25in;} |
| 1913 | | @list l12:level9 |
| 1914 | | {mso-level-tab-stop:4.5in; |
| 1915 | | mso-level-number-position:left; |
| 1916 | | text-indent:-.25in;} |
| 1917 | | @list l13 |
| 1918 | | {mso-list-id:742676264; |
| 1919 | | mso-list-template-ids:713467934;} |
| 1920 | | @list l13:level1 |
| 1921 | | {mso-level-tab-stop:none; |
| 1922 | | mso-level-number-position:left; |
| 1923 | | margin-left:45.0pt; |
| 1924 | | text-indent:-.25in;} |
| 1925 | | @list l13:level2 |
| 1926 | | {mso-level-number-format:alpha-lower; |
| 1927 | | mso-level-tab-stop:1.0in; |
| 1928 | | mso-level-number-position:left; |
| 1929 | | text-indent:-.25in; |
| 1930 | | mso-ansi-font-size:12.0pt; |
| 1931 | | font-family:"Times New Roman",serif; |
| 1932 | | mso-ansi-font-weight:normal; |
| 1933 | | mso-ansi-font-style:normal;} |
| 1934 | | @list l13:level3 |
| 1935 | | {mso-level-tab-stop:1.5in; |
| 1936 | | mso-level-number-position:left; |
| 1937 | | text-indent:-.25in;} |
| 1938 | | @list l13:level4 |
| 1939 | | {mso-level-number-format:alpha-lower; |
| 1940 | | mso-level-tab-stop:2.0in; |
| 1941 | | mso-level-number-position:left; |
| 1942 | | text-indent:-.25in;} |
| 1943 | | @list l13:level5 |
| 1944 | | {mso-level-tab-stop:2.5in; |
| 1945 | | mso-level-number-position:left; |
| 1946 | | text-indent:-.25in;} |
| 1947 | | @list l13:level6 |
| 1948 | | {mso-level-tab-stop:3.0in; |
| 1949 | | mso-level-number-position:left; |
| 1950 | | text-indent:-.25in;} |
| 1951 | | @list l13:level7 |
| 1952 | | {mso-level-tab-stop:3.5in; |
| 1953 | | mso-level-number-position:left; |
| 1954 | | text-indent:-.25in;} |
| 1955 | | @list l13:level8 |
| 1956 | | {mso-level-tab-stop:4.0in; |
| 1957 | | mso-level-number-position:left; |
| 1958 | | text-indent:-.25in;} |
| 1959 | | @list l13:level9 |
| 1960 | | {mso-level-tab-stop:4.5in; |
| 1961 | | mso-level-number-position:left; |
| 1962 | | text-indent:-.25in;} |
| 1963 | | @list l14 |
| 1964 | | {mso-list-id:850026630; |
| 1965 | | mso-list-type:hybrid; |
| 1966 | | mso-list-template-ids:120980256 67698703 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;} |
| 1967 | | @list l14:level1 |
| 1968 | | {mso-level-tab-stop:none; |
| 1969 | | mso-level-number-position:left; |
| 1970 | | text-indent:-.25in;} |
| 1971 | | @list l14:level2 |
| 1972 | | {mso-level-number-format:alpha-lower; |
| 1973 | | mso-level-tab-stop:none; |
| 1974 | | mso-level-number-position:left; |
| 1975 | | text-indent:-.25in;} |
| 1976 | | @list l14:level3 |
| 1977 | | {mso-level-tab-stop:1.5in; |
| 1978 | | mso-level-number-position:left; |
| 1979 | | text-indent:-.25in;} |
| 1980 | | @list l14:level4 |
| 1981 | | {mso-level-tab-stop:2.0in; |
| 1982 | | mso-level-number-position:left; |
| 1983 | | text-indent:-.25in;} |
| 1984 | | @list l14:level5 |
| 1985 | | {mso-level-tab-stop:2.5in; |
| 1986 | | mso-level-number-position:left; |
| 1987 | | text-indent:-.25in;} |
| 1988 | | @list l14:level6 |
| 1989 | | {mso-level-tab-stop:3.0in; |
| 1990 | | mso-level-number-position:left; |
| 1991 | | text-indent:-.25in;} |
| 1992 | | @list l14:level7 |
| 1993 | | {mso-level-tab-stop:3.5in; |
| 1994 | | mso-level-number-position:left; |
| 1995 | | text-indent:-.25in;} |
| 1996 | | @list l14:level8 |
| 1997 | | {mso-level-tab-stop:4.0in; |
| 1998 | | mso-level-number-position:left; |
| 1999 | | text-indent:-.25in;} |
| 2000 | | @list l14:level9 |
| 2001 | | {mso-level-tab-stop:4.5in; |
| 2002 | | mso-level-number-position:left; |
| 2003 | | text-indent:-.25in;} |
| 2004 | | @list l15 |
| 2005 | | {mso-list-id:884020553; |
| 2006 | | mso-list-template-ids:1740294536;} |
| 2007 | | @list l15:level1 |
| 2008 | | {mso-level-number-format:bullet; |
| 2009 | | mso-level-text:; |
| 2010 | | mso-level-tab-stop:.5in; |
| 2011 | | mso-level-number-position:left; |
| 2012 | | text-indent:-.25in; |
| 2013 | | mso-ansi-font-size:10.0pt; |
| 2014 | | font-family:Symbol;} |
| 2015 | | @list l15:level2 |
| 2016 | | {mso-level-number-format:bullet; |
| 2017 | | mso-level-text:o; |
| 2018 | | mso-level-tab-stop:1.0in; |
| 2019 | | mso-level-number-position:left; |
| 2020 | | text-indent:-.25in; |
| 2021 | | mso-ansi-font-size:10.0pt; |
| 2022 | | font-family:"Courier New"; |
| 2023 | | mso-bidi-font-family:"Times New Roman";} |
| 2024 | | @list l15:level3 |
| 2025 | | {mso-level-number-format:bullet; |
| 2026 | | mso-level-text:; |
| 2027 | | mso-level-tab-stop:1.5in; |
| 2028 | | mso-level-number-position:left; |
| 2029 | | text-indent:-.25in; |
| 2030 | | mso-ansi-font-size:10.0pt; |
| 2031 | | font-family:Wingdings;} |
| 2032 | | @list l15:level4 |
| 2033 | | {mso-level-number-format:bullet; |
| 2034 | | mso-level-text:; |
| 2035 | | mso-level-tab-stop:2.0in; |
| 2036 | | mso-level-number-position:left; |
| 2037 | | text-indent:-.25in; |
| 2038 | | mso-ansi-font-size:10.0pt; |
| 2039 | | font-family:Wingdings;} |
| 2040 | | @list l15:level5 |
| 2041 | | {mso-level-number-format:bullet; |
| 2042 | | mso-level-text:; |
| 2043 | | mso-level-tab-stop:2.5in; |
| 2044 | | mso-level-number-position:left; |
| 2045 | | text-indent:-.25in; |
| 2046 | | mso-ansi-font-size:10.0pt; |
| 2047 | | font-family:Wingdings;} |
| 2048 | | @list l15:level6 |
| 2049 | | {mso-level-number-format:bullet; |
| 2050 | | mso-level-text:; |
| 2051 | | mso-level-tab-stop:3.0in; |
| 2052 | | mso-level-number-position:left; |
| 2053 | | text-indent:-.25in; |
| 2054 | | mso-ansi-font-size:10.0pt; |
| 2055 | | font-family:Wingdings;} |
| 2056 | | @list l15:level7 |
| 2057 | | {mso-level-number-format:bullet; |
| 2058 | | mso-level-text:; |
| 2059 | | mso-level-tab-stop:3.5in; |
| 2060 | | mso-level-number-position:left; |
| 2061 | | text-indent:-.25in; |
| 2062 | | mso-ansi-font-size:10.0pt; |
| 2063 | | font-family:Wingdings;} |
| 2064 | | @list l15:level8 |
| 2065 | | {mso-level-number-format:bullet; |
| 2066 | | mso-level-text:; |
| 2067 | | mso-level-tab-stop:4.0in; |
| 2068 | | mso-level-number-position:left; |
| 2069 | | text-indent:-.25in; |
| 2070 | | mso-ansi-font-size:10.0pt; |
| 2071 | | font-family:Wingdings;} |
| 2072 | | @list l15:level9 |
| 2073 | | {mso-level-number-format:bullet; |
| 2074 | | mso-level-text:; |
| 2075 | | mso-level-tab-stop:4.5in; |
| 2076 | | mso-level-number-position:left; |
| 2077 | | text-indent:-.25in; |
| 2078 | | mso-ansi-font-size:10.0pt; |
| 2079 | | font-family:Wingdings;} |
| 2080 | | @list l16 |
| 2081 | | {mso-list-id:919948450; |
| 2082 | | mso-list-template-ids:-445226636;} |
| 2083 | | @list l16:level1 |
| 2084 | | {mso-level-tab-stop:none; |
| 2085 | | mso-level-number-position:left; |
| 2086 | | text-indent:-.25in;} |
| 2087 | | @list l16:level2 |
| 2088 | | {mso-level-number-format:alpha-lower; |
| 2089 | | mso-level-tab-stop:1.0in; |
| 2090 | | mso-level-number-position:left; |
| 2091 | | text-indent:-.25in;} |
| 2092 | | @list l16:level3 |
| 2093 | | {mso-level-tab-stop:1.5in; |
| 2094 | | mso-level-number-position:left; |
| 2095 | | text-indent:-.25in;} |
| 2096 | | @list l16:level4 |
| 2097 | | {mso-level-number-format:alpha-lower; |
| 2098 | | mso-level-tab-stop:2.0in; |
| 2099 | | mso-level-number-position:left; |
| 2100 | | text-indent:-.25in;} |
| 2101 | | @list l16:level5 |
| 2102 | | {mso-level-tab-stop:2.5in; |
| 2103 | | mso-level-number-position:left; |
| 2104 | | text-indent:-.25in;} |
| 2105 | | @list l16:level6 |
| 2106 | | {mso-level-tab-stop:3.0in; |
| 2107 | | mso-level-number-position:left; |
| 2108 | | text-indent:-.25in;} |
| 2109 | | @list l16:level7 |
| 2110 | | {mso-level-tab-stop:3.5in; |
| 2111 | | mso-level-number-position:left; |
| 2112 | | text-indent:-.25in;} |
| 2113 | | @list l16:level8 |
| 2114 | | {mso-level-tab-stop:4.0in; |
| 2115 | | mso-level-number-position:left; |
| 2116 | | text-indent:-.25in;} |
| 2117 | | @list l16:level9 |
| 2118 | | {mso-level-tab-stop:4.5in; |
| 2119 | | mso-level-number-position:left; |
| 2120 | | text-indent:-.25in;} |
| 2121 | | @list l17 |
| 2122 | | {mso-list-id:1030640961; |
| 2123 | | mso-list-template-ids:-913388448;} |
| 2124 | | @list l17:level1 |
| 2125 | | {mso-level-number-format:bullet; |
| 2126 | | mso-level-text:; |
| 2127 | | mso-level-tab-stop:.5in; |
| 2128 | | mso-level-number-position:left; |
| 2129 | | text-indent:-.25in; |
| 2130 | | mso-ansi-font-size:10.0pt; |
| 2131 | | font-family:Symbol;} |
| 2132 | | @list l17:level2 |
| 2133 | | {mso-level-number-format:bullet; |
| 2134 | | mso-level-text:o; |
| 2135 | | mso-level-tab-stop:1.0in; |
| 2136 | | mso-level-number-position:left; |
| 2137 | | text-indent:-.25in; |
| 2138 | | mso-ansi-font-size:10.0pt; |
| 2139 | | font-family:"Courier New"; |
| 2140 | | mso-bidi-font-family:"Times New Roman";} |
| 2141 | | @list l17:level3 |
| 2142 | | {mso-level-number-format:bullet; |
| 2143 | | mso-level-text:; |
| 2144 | | mso-level-tab-stop:1.5in; |
| 2145 | | mso-level-number-position:left; |
| 2146 | | text-indent:-.25in; |
| 2147 | | mso-ansi-font-size:10.0pt; |
| 2148 | | font-family:Wingdings;} |
| 2149 | | @list l17:level4 |
| 2150 | | {mso-level-number-format:bullet; |
| 2151 | | mso-level-text:; |
| 2152 | | mso-level-tab-stop:2.0in; |
| 2153 | | mso-level-number-position:left; |
| 2154 | | text-indent:-.25in; |
| 2155 | | mso-ansi-font-size:10.0pt; |
| 2156 | | font-family:Wingdings;} |
| 2157 | | @list l17:level5 |
| 2158 | | {mso-level-number-format:bullet; |
| 2159 | | mso-level-text:; |
| 2160 | | mso-level-tab-stop:2.5in; |
| 2161 | | mso-level-number-position:left; |
| 2162 | | text-indent:-.25in; |
| 2163 | | mso-ansi-font-size:10.0pt; |
| 2164 | | font-family:Wingdings;} |
| 2165 | | @list l17:level6 |
| 2166 | | {mso-level-number-format:bullet; |
| 2167 | | mso-level-text:; |
| 2168 | | mso-level-tab-stop:3.0in; |
| 2169 | | mso-level-number-position:left; |
| 2170 | | text-indent:-.25in; |
| 2171 | | mso-ansi-font-size:10.0pt; |
| 2172 | | font-family:Wingdings;} |
| 2173 | | @list l17:level7 |
| 2174 | | {mso-level-number-format:bullet; |
| 2175 | | mso-level-text:; |
| 2176 | | mso-level-tab-stop:3.5in; |
| 2177 | | mso-level-number-position:left; |
| 2178 | | text-indent:-.25in; |
| 2179 | | mso-ansi-font-size:10.0pt; |
| 2180 | | font-family:Wingdings;} |
| 2181 | | @list l17:level8 |
| 2182 | | {mso-level-number-format:bullet; |
| 2183 | | mso-level-text:; |
| 2184 | | mso-level-tab-stop:4.0in; |
| 2185 | | mso-level-number-position:left; |
| 2186 | | text-indent:-.25in; |
| 2187 | | mso-ansi-font-size:10.0pt; |
| 2188 | | font-family:Wingdings;} |
| 2189 | | @list l17:level9 |
| 2190 | | {mso-level-number-format:bullet; |
| 2191 | | mso-level-text:; |
| 2192 | | mso-level-tab-stop:4.5in; |
| 2193 | | mso-level-number-position:left; |
| 2194 | | text-indent:-.25in; |
| 2195 | | mso-ansi-font-size:10.0pt; |
| 2196 | | font-family:Wingdings;} |
| 2197 | | @list l18 |
| 2198 | | {mso-list-id:1035230400; |
| 2199 | | mso-list-type:hybrid; |
| 2200 | | mso-list-template-ids:-2012591744 67698703 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;} |
| | 2255 | mso-list-template-ids:2031237610 67698703 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;} |
| 3163 | | section, which provides a hierarchical view of the current project on |
| 3164 | | the left and the <a |
| 3165 | | href="#Data_Frame">GSAS-II data editing</a> section, which shows the contents of |
| 3166 | | a particular section of the project, where values can be examined and changed; |
| 3167 | | The second is the <a href="#Plots">GSAS-II Plots</a> window, which shows graphical |
| 3168 | | representations of the results. The third is a console window, which has printout information |
| 3169 | | that can be selected, cut & pasted into a document. <o:p></o:p></span></p> |
| 3170 | | |
| 3171 | | <h2><a name="Index">Help Index</a></h2> |
| 3172 | | <OL> |
| 3173 | | <LI><a href="#Tutorials">Learning GSAS-II: tutorials</a></LI> |
| 3174 | | <LI><a href="#Data_tree">Application windows</a></LI> |
| 3175 | | <LI><a href="#main_menu">Main menu commands</a></LI> |
| 3176 | | <LI>Data Tree headings, graphics windows and menu commands</LI> |
| 3177 | | <OL type="A"> |
| 3178 | | <LI><a href="#Data_tree_items">Top-level </a>Data Tree headings</LI> |
| 3179 | | <LI><a href="#Phase">Phase </a>Data Tree headings</LI> |
| 3180 | | <LI><a href="#IMG">Image (IMG) </a>Data Tree headings</LI> |
| 3181 | | <LI><a href="#PWDR">Powder histogram (PWDR) </a>Data Tree |
| 3182 | | headings</LI> |
| 3183 | | <UL> |
| 3184 | | <LI><a href="#PWDR_Comments">Comments</a></li> |
| 3185 | | <LI><a href="#PWDR_Limits">Limits</a></li> |
| 3186 | | <LI><a href="#PWDR_Background">Background</a></li> |
| 3187 | | <LI><a href="#PWDR_Instrument_Parameters">Instrument Parameters</a></li> |
| 3188 | | <LI><a href="#PWDR_Sample_Parameters">Sample Parameters</a></li> |
| 3189 | | <LI><a href="#PWDR_Peak_List">Peak List</a></li> |
| 3190 | | <LI><a href="#PWDR_Index_Peak_List">Index Peak List</a></li> |
| 3191 | | <LI><a href="#PWDR_Unit_Cells_List">Unit Cells List</a></li> |
| 3192 | | <LI><a href="#PWDR_Reflection_Lists">Reflection Lists</a></li> |
| 3193 | | </UL> |
| 3194 | | |
| 3195 | | <LI><a href="#HKLF">Single Crystal histogram (HKLF)</a> Data Tree |
| 3196 | | headings</LI> |
| 3197 | | <UL> |
| 3198 | | <LI><a href="#HKLF_Instrument_Parameters">Instrument Parameters</a></li> |
| 3199 | | <LI><a href="#HKLF_HKL_Plot_Controls">HKL Plot Controls</a></li> |
| 3200 | | <LI><a href="#HKLF_Reflection_List">Reflection List</a></li> |
| 3201 | | </UL> |
| 3202 | | <LI><a href="#PDF">Pair Distribution Functions (PDF) </a>Data Tree headings</LI> |
| 3203 | | <LI><a href="#PKS">Powder Peaks (PKS) </a>Data Tree headings</LI> |
| 3204 | | <LI><a href="#SASD">Small Angle Scattering (SASD) </a>Data Tree |
| 3205 | | headings</LI> |
| 3206 | | </OL> |
| 3207 | | <LI>Other: <a href="#Mac">Macintosh notes</a>, |
| 3208 | | <a href="#Preferences">Configuration options</a> |
| 3209 | | and <a href="#Programmers">Programmers documentation</a> |
| 3210 | | </OL> |
| 3211 | | |
| 3212 | | |
| 3213 | | <h2><a name="Tutorials"><strong>Learning GSAS-II: Tutorials</strong></a></h2> |
| 3214 | | |
| 3215 | | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:"Times New Roman"'>The |
| 3216 | | best way to learn about how different sections of GSAS-II is used is |
| 3217 | | to work through tutorials. A list of available tutorial topics appears on a |
| 3218 | | <A href="Tutorials.html">separate web page</A>. |
| 3219 | | |
| 3220 | | <P> |
| | 2885 | section, which provides a hierarchical view of the current project on the left |
| | 2886 | and the <a href="#Data_Frame">GSAS-II data editing</a> section, which shows the |
| | 2887 | contents of a particular section of the project, where values can be examined |
| | 2888 | and changed; The second is the <a href="#Plots">GSAS-II Plots</a> window, which |
| | 2889 | shows graphical representations of the results. The third is a console window, |
| | 2890 | which has printout information that can be selected, cut & pasted into a |
| | 2891 | document. <o:p></o:p></span></p> |
| | 2892 | |
| | 2893 | <h2><a name=Index><span style='mso-fareast-font-family:"Times New Roman"'>Help |
| | 2894 | Index</span></a><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h2> |
| | 2895 | |
| | 2896 | <ol start=1 type=1> |
| | 2897 | <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto; |
| | 2898 | mso-list:l15 level1 lfo1;tab-stops:list .5in'><span style='mso-fareast-font-family: |
| | 2899 | "Times New Roman"'><a href="#Tutorials">Learning GSAS-II: tutorials</a><o:p></o:p></span></li> |
| | 2900 | <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto; |
| | 2901 | mso-list:l15 level1 lfo1;tab-stops:list .5in'><span style='mso-fareast-font-family: |
| | 2902 | "Times New Roman"'><a href="#Data_tree">Application windows</a><o:p></o:p></span></li> |
| | 2903 | <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto; |
| | 2904 | mso-list:l15 level1 lfo1;tab-stops:list .5in'><span style='mso-fareast-font-family: |
| | 2905 | "Times New Roman"'><a href="#main_menu">Main menu commands</a><o:p></o:p></span></li> |
| | 2906 | <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto; |
| | 2907 | mso-list:l15 level1 lfo1;tab-stops:list .5in'><span style='mso-fareast-font-family: |
| | 2908 | "Times New Roman"'>Data Tree headings, graphics windows and menu commands<o:p></o:p></span></li> |
| | 2909 | <ol start=1 type=A> |
| | 2910 | <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt: |
| | 2911 | auto;mso-list:l15 level2 lfo1;tab-stops:list 1.0in'><span |
| | 2912 | style='mso-fareast-font-family:"Times New Roman"'><a |
| | 2913 | href="#Data_tree_items">Top-level </a>Data Tree headings<o:p></o:p></span></li> |
| | 2914 | <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt: |
| | 2915 | auto;mso-list:l15 level2 lfo1;tab-stops:list 1.0in'><span |
| | 2916 | style='mso-fareast-font-family:"Times New Roman"'><a href="#Phase">Phase </a>Data |
| | 2917 | Tree headings<o:p></o:p></span></li> |
| | 2918 | <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt: |
| | 2919 | auto;mso-list:l15 level2 lfo1;tab-stops:list 1.0in'><span |
| | 2920 | style='mso-fareast-font-family:"Times New Roman"'><a href="#IMG">Image |
| | 2921 | (IMG) </a>Data Tree headings<o:p></o:p></span></li> |
| | 2922 | <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt: |
| | 2923 | auto;mso-list:l15 level2 lfo1;tab-stops:list 1.0in'><span |
| | 2924 | style='mso-fareast-font-family:"Times New Roman"'><a href="#PWDR">Powder |
| | 2925 | histogram (PWDR) </a>Data Tree headings<o:p></o:p></span></li> |
| | 2926 | <ul type=square> |
| | 2927 | <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt: |
| | 2928 | auto;mso-list:l15 level3 lfo1;tab-stops:list 1.5in'><span |
| | 2929 | style='mso-fareast-font-family:"Times New Roman"'><a |
| | 2930 | href="#PWDR_Comments">Comments</a><o:p></o:p></span></li> |
| | 2931 | <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt: |
| | 2932 | auto;mso-list:l15 level3 lfo1;tab-stops:list 1.5in'><span |
| | 2933 | style='mso-fareast-font-family:"Times New Roman"'><a href="#PWDR_Limits">Limits</a><o:p></o:p></span></li> |
| | 2934 | <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt: |
| | 2935 | auto;mso-list:l15 level3 lfo1;tab-stops:list 1.5in'><span |
| | 2936 | style='mso-fareast-font-family:"Times New Roman"'><a |
| | 2937 | href="#PWDR_Background">Background</a><o:p></o:p></span></li> |
| | 2938 | <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt: |
| | 2939 | auto;mso-list:l15 level3 lfo1;tab-stops:list 1.5in'><span |
| | 2940 | style='mso-fareast-font-family:"Times New Roman"'><a |
| | 2941 | href="#PWDR_Instrument_Parameters">Instrument Parameters</a><o:p></o:p></span></li> |
| | 2942 | <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt: |
| | 2943 | auto;mso-list:l15 level3 lfo1;tab-stops:list 1.5in'><span |
| | 2944 | style='mso-fareast-font-family:"Times New Roman"'><a |
| | 2945 | href="#PWDR_Sample_Parameters">Sample Parameters</a><o:p></o:p></span></li> |
| | 2946 | <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt: |
| | 2947 | auto;mso-list:l15 level3 lfo1;tab-stops:list 1.5in'><span |
| | 2948 | style='mso-fareast-font-family:"Times New Roman"'><a |
| | 2949 | href="#PWDR_Peak_List">Peak List</a><o:p></o:p></span></li> |
| | 2950 | <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt: |
| | 2951 | auto;mso-list:l15 level3 lfo1;tab-stops:list 1.5in'><span |
| | 2952 | style='mso-fareast-font-family:"Times New Roman"'><a |
| | 2953 | href="#PWDR_Index_Peak_List">Index Peak List</a><o:p></o:p></span></li> |
| | 2954 | <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt: |
| | 2955 | auto;mso-list:l15 level3 lfo1;tab-stops:list 1.5in'><span |
| | 2956 | style='mso-fareast-font-family:"Times New Roman"'><a |
| | 2957 | href="#PWDR_Unit_Cells_List">Unit Cells List</a><o:p></o:p></span></li> |
| | 2958 | <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt: |
| | 2959 | auto;mso-list:l15 level3 lfo1;tab-stops:list 1.5in'><span |
| | 2960 | style='mso-fareast-font-family:"Times New Roman"'><a |
| | 2961 | href="#PWDR_Reflection_Lists">Reflection Lists</a><o:p></o:p></span></li> |
| | 2962 | </ul> |
| | 2963 | <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt: |
| | 2964 | auto;mso-list:l15 level2 lfo1;tab-stops:list 1.0in'><span |
| | 2965 | style='mso-fareast-font-family:"Times New Roman"'><a href="#HKLF">Single |
| | 2966 | Crystal histogram (HKLF)</a> Data Tree headings<o:p></o:p></span></li> |
| | 2967 | <ul type=square> |
| | 2968 | <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt: |
| | 2969 | auto;mso-list:l15 level3 lfo1;tab-stops:list 1.5in'><span |
| | 2970 | style='mso-fareast-font-family:"Times New Roman"'><a |
| | 2971 | href="#HKLF_Instrument_Parameters">Instrument Parameters</a><o:p></o:p></span></li> |
| | 2972 | <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt: |
| | 2973 | auto;mso-list:l15 level3 lfo1;tab-stops:list 1.5in'><span |
| | 2974 | style='mso-fareast-font-family:"Times New Roman"'><a |
| | 2975 | href="#HKLF_HKL_Plot_Controls">HKL Plot Controls</a><o:p></o:p></span></li> |
| | 2976 | <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt: |
| | 2977 | auto;mso-list:l15 level3 lfo1;tab-stops:list 1.5in'><span |
| | 2978 | style='mso-fareast-font-family:"Times New Roman"'><a |
| | 2979 | href="#HKLF_Reflection_List">Reflection List</a><o:p></o:p></span></li> |
| | 2980 | </ul> |
| | 2981 | <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt: |
| | 2982 | auto;mso-list:l15 level2 lfo1;tab-stops:list 1.0in'><span |
| | 2983 | style='mso-fareast-font-family:"Times New Roman"'><a href="#PDF">Pair |
| | 2984 | Distribution Functions (PDF) </a>Data Tree headings<o:p></o:p></span></li> |
| | 2985 | <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt: |
| | 2986 | auto;mso-list:l15 level2 lfo1;tab-stops:list 1.0in'><span |
| | 2987 | style='mso-fareast-font-family:"Times New Roman"'><a href="#PKS">Powder |
| | 2988 | Peaks (PKS) </a>Data Tree headings<o:p></o:p></span></li> |
| | 2989 | <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt: |
| | 2990 | auto;mso-list:l15 level2 lfo1;tab-stops:list 1.0in'><span |
| | 2991 | style='mso-fareast-font-family:"Times New Roman"'><a href="#SASD">Small |
| | 2992 | Angle Scattering (SASD) </a>Data Tree headings<o:p></o:p></span></li> |
| | 2993 | </ol> |
| | 2994 | <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto; |
| | 2995 | mso-list:l15 level1 lfo1;tab-stops:list .5in'><span style='mso-fareast-font-family: |
| | 2996 | "Times New Roman"'>Other: <a href="#Mac">Macintosh notes</a>, <a |
| | 2997 | href="#Preferences">Configuration options</a> and <a href="#Programmers">Programmers |
| | 2998 | documentation</a> <o:p></o:p></span></li> |
| | 2999 | </ol> |
| | 3000 | |
| | 3001 | <h2><a name=Tutorials><strong><span style='mso-fareast-font-family:"Times New Roman"'>Learning |
| | 3002 | GSAS-II: Tutorials</span></strong></a><span style='mso-bookmark:Tutorials'></span><span |
| | 3003 | style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h2> |
| | 3004 | |
| | 3005 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3006 | "Times New Roman"'>The best way to learn about how different sections of |
| | 3007 | GSAS-II is used is to work through tutorials. A list of available tutorial |
| | 3008 | topics appears on a <a href="Tutorials.html">separate web page</a>. <o:p></o:p></span></p> |
| | 3009 | |
| | 3010 | <div class=MsoNormal align=center style='text-align:center'><span |
| | 3011 | style='mso-fareast-font-family:"Times New Roman"'> |
| 3334 | | <h2><a name="main_menu">4. Main GSAS-II menu commands</a></h2> |
| 3335 | | <OL style='margin-left:.5in'> |
| 3336 | | <LI>Menu <B>File</B> |
| 3337 | | <DL style='margin-left:.2in'> |
| 3338 | | <DT><b>Open project…</b> |
| 3339 | | <DD>Open a previously saved GSAS-II project file |
| 3340 | | ({project}.gpx). If you currently have a project file open, you |
| 3341 | | are asked if it is OK to overwrite it; Cancel will cancel the |
| 3342 | | read process. |
| 3343 | | <P>Note that as files are saved, copies of the previous version |
| 3344 | | are saved as backup files, named as {project}.bak{<i>i</i>}.gpx, |
| 3345 | | where <i>i</i> starts as 0 and is increased after each save |
| 3346 | | operation. |
| 3347 | | NB: you may open a backup .gpx file (e.g. name.bak3.gpx) to return |
| 3348 | | to a previous version of your project, but if you do so, it is |
| 3349 | | best to immediately use the <b'>Save As...</b> menu command (you |
| 3350 | | may wish to use name.gpx to overwrite the current version or |
| 3351 | | select a new name.) If you forget specify a project name, then |
| 3352 | | name.bak3 will be considered the project name and backups will |
| 3353 | | then be named name.bak3.bak0.gpx, etc.</p> |
| 3354 | | <DT><b>Save project</b> |
| 3355 | | <DD>Save the current project. If this is a new project that has not |
| 3356 | | yet been saved, you will be prompted for a new name in a file |
| 3357 | | dialog (you may optionally change the directory in that |
| 3358 | | dialog). If the file exists, you will be asked if it is OK to |
| 3359 | | overwrite it. Once a file name has been used to read or save a |
| 3360 | | project, the name is shown |
| 3361 | | after ‘Loaded Data:’ in the first item in the data tree. |
| 3362 | | <DT><b>Save Project as...</b> |
| 3363 | | <DD>Save the current project in a |
| 3364 | | specified project file. You will be prompted for a new name in a file |
| 3365 | | dialog (you may optionally change the directory in that |
| 3366 | | dialog). If the file exists, you will be asked if it is OK to |
| 3367 | | overwrite it. |
| 3368 | | <DT><b>New Project</b> |
| 3369 | | <DD>Discards any changes made to the current project since the |
| 3370 | | last save and creates a new empty project. |
| 3371 | | <DT><b>Preferences</b> |
| 3372 | | <DD>Provides access to GSAS-II configuration settings, as |
| 3373 | | described in the <a href=#Preferences>Configuration |
| 3374 | | Variables</a> section. |
| 3375 | | <DT><b>Quit</b> |
| 3376 | | <DD>Exit the GSAS-II program. Discards any changes made to the current project since the |
| 3377 | | last save. You can also exit GSAS-II by pressing the red X in |
| 3378 | | the upper right (Windows) or left (Mac). |
| 3379 | | </DL> |
| 3380 | | |
| 3381 | | <LI>Menu <B>Data</B> |
| 3382 | | <DL style='margin-left:.2in'> |
| 3383 | | <DT><b>Read Powder Pattern Peaks…</b> |
| 3384 | | <DD>Read in a list of powder pattern peak positions as either a |
| 3385 | | d-spacing table or a set of 2theta positions; these can be used |
| 3386 | | in GSAS-II powder pattern indexing. |
| 3387 | | <DT><b>Sum powder data</b> |
| 3388 | | <DD>Form the sum of |
| 3389 | | previously read powder patterns; each with a multiplier. Can be used to |
| 3390 | | accumulate data, subtract background or empty container patterns, etc. Patterns |
| 3391 | | used to form the sum must be of identical range and step size. Result is a new |
| 3392 | | PWDR entry in the GSAS-II data tree. |
| 3393 | | <DT><b>Sum image data</b> |
| 3394 | | <DD>Form the sum of previously |
| 3395 | | read 2-D images; each with a multiplier. Can be used to accumulate data, |
| 3396 | | subtract background or empty container patterns, etc. Images used to form the |
| 3397 | | sum must be of identical size and source. Result is a new IMG entry in the |
| 3398 | | GSAS-II data tree, and a GSAS-II image file is written for future use. |
| 3399 | | <DT><b>Add new phase </b> |
| 3400 | | <DD>This begins the creation of a new phase in the data tree |
| 3401 | | (under Phases). You are first prompted in a dialog box for a |
| 3402 | | name to be assigned to the new phase. Then the Phase/<a |
| 3403 | | href="#General">General</a></b> tab is opened for this phase, |
| 3404 | | where you should first select the phase type, the enter the |
| 3405 | | space group symbol and then the lattice parameters. |
| 3406 | | <BR>Note that nonstandard space group symbols are permitted; |
| 3407 | | space group names must have spaces between the axial fields |
| 3408 | | (e.g. use ‘P n a 21’ not ‘Pna21’). |
| 3409 | | <DT><b>Delete phase</b> |
| 3410 | | <DD>This will remove a phase from the data tree. A dialog box will |
| 3411 | | present the list of phases; pick one (or more) to delete. |
| 3412 | | <DT><b>Rename tree item</b> |
| 3413 | | <DD>Rename a histogram entry. This should only be done before the |
| 3414 | | histogram is used in any phases: e.g. only rename data |
| 3415 | | immediately after reading. |
| 3416 | | <DT><b>Delete tree item</b> |
| 3417 | | <DD>This will remove an item from the data tree. A dialog box with |
| 3418 | | a list of choices for histograms is presented. Be sure to remove |
| 3419 | | a histograms from all phases before deleting it from the tree. |
| 3420 | | <DT><b>Expand tree item</b> |
| 3421 | | <DD>This will show child entries for specified type of items |
| 3422 | | (Images, Powder patterns, etc.)</DD> |
| 3423 | | <DT><b>Move tree item</b> |
| 3424 | | <DD>Move classes of Tree items around in the tree. Individual |
| 3425 | | top-level tree items can be moved using the left mouse button. |
| 3426 | | </DD> |
| 3427 | | |
| 3428 | | </DL> |
| 3429 | | |
| 3430 | | <LI>Menu <B><A name="Calculate_menu">Calculate</A></B> |
| 3431 | | <DL style='margin-left:.2in'> |
| 3432 | | <DT><b>Setup PDFs</b> |
| 3433 | | <DD>This creates the pair distribution function (PDF) controls for |
| 3434 | | each powder pattern selected in the dialog box, but does not compute |
| 3435 | | the PDF, which must be done from <b><a |
| 3436 | | href="#PDF">PDF tree entries</a></b>. See <b><a |
| 3437 | | href="#PDF_Controls">PDF Controls</a></b> for information on the PDF |
| 3438 | | input. |
| 3439 | | <DT><b>View LS parms</b> |
| 3440 | | <DD>This shows a dialog box with all the parameters for your |
| 3441 | | project; those to be refined are flagged ‘True’, otherwise |
| 3442 | | ‘False’. Blanks indicate parameters that are not refinable. The |
| 3443 | | total number of refined parameters is also shown at the top of the |
| 3444 | | list. The value of each parameter is also given. The parameter names |
| 3445 | | are of the form ‘p:h:name:id’ where ‘p’ is the phase index, ‘h’ is |
| 3446 | | the histogram index and ‘id’ is the item index (if needed). Indexes |
| 3447 | | all begin with ‘0’ (zero). |
| 3448 | | <P> |
| 3449 | | Note that for atom positions, the coordinate values (named as |
| 3450 | | ‘p::A<i>w</i>:n’, where p is the phase number, n is the atom number |
| 3451 | | and <i>w</i> is x, y or z) is |
| 3452 | | not a refinable parameter, but the shift in the value is. The |
| 3453 | | refined parameters are ‘p::A<i>w</i>:n’. |
| 3454 | | The reason this is done is that by treating an atom |
| 3455 | | position as x+dx,y+dy,z+dz where the “d” values indicate shifts from |
| 3456 | | the starting position and the shifts |
| 3457 | | are refined rather than the x,y, or z values is that this simplifies |
| 3458 | | symmetry constraints. As an example, suppose we have an atom on |
| 3459 | | a symmetry constrained site, x,1/2-x,z. The process needed to define |
| 3460 | | this constraint, so |
| 3461 | | that if x moves positively y has to move negatively by the same |
| 3462 | | amount would be messy. With refinement of shifts, all we need to do is constrain dy (‘0::dAy:n’) |
| 3463 | | to be equal to -dx (-1*‘0::dAx:n’). |
| 3464 | | <P> |
| 3465 | | Press the window exit button to exit this dialog box. |
| 3466 | | <DT><b>Refine</b> |
| 3467 | | <DD>This performs the refinement (Pawley/Rietveld or single |
| 3468 | | crystal) according to the controls set in the <b><a |
| 3469 | | href="#Controls">Controls</a></b> data tree item. |
| 3470 | | <DT><b>Sequential refine</b> |
| 3471 | | <DD>This starts a sequential refinement with the data sets |
| 3472 | | selected in the <b><a href="#Controls">Controls</a></b> data tree |
| 3473 | | item. |
| 3474 | | </DL> |
| 3475 | | |
| 3476 | | <LI>Menu <B>Import</B> |
| 3477 | | <P>GSAS-II uses separate routines to read in information from external |
| 3478 | | files that can be created and customized easily. See the GSAS-II |
| 3479 | | Import Modules section of the <a |
| 3480 | | href=#Programmers><strong>Programmers documentation</strong></a> for |
| 3481 | | more information on this. Since it is easy to support new formats, |
| 3482 | | the documentation below may not list all supported formats. |
| 3483 | | <DL style='margin-left:.2in'> |
| 3484 | | <DT><b>Image</b> |
| 3485 | | <DD>Read in 2-D powder diffraction images (multiple |
| 3486 | | patterns can be selected). A sub menu appears with choices for |
| 3487 | | import of data. Each entry when selected with the mouse shows |
| 3488 | | further submenus with specific imports that are available. Any of |
| 3489 | | these files can be accessed from a zip file. GSAS-II can read many |
| 3490 | | different image file formats including MAR345 files, Quantum ADSC |
| 3491 | | files, and tiff files from Perkin-Elmer, Pilatus, and GE. Although |
| 3492 | | many of these formats have data fields that should contain relevant information |
| 3493 | | for the exposure (e.g. wavelength), these are rarely filled in |
| 3494 | | correctly by the data acquisition software. Thus, you should have |
| 3495 | | separately noted this information as it will be needed |
| 3496 | | <DT><b>Phase</b> |
| 3497 | | <DD>Creates a new phase by reading unit cell/symmetry/atom |
| 3498 | | coordinate information. GSAS-II can read information from a number |
| 3499 | | of different format files including: |
| 3500 | | <DL> |
| 3501 | | <DT>GSAS .EXP |
| 3502 | | <DD>This reads one phase from a (old) GSAS experiment file |
| 3503 | | (name.EXP). The file name is found in a directory dialog; you can |
| 3504 | | change directories as needed. Only .EXP (or .exp) file names are |
| 3505 | | shown. If the selected file has more than one phase, a dialog is |
| 3506 | | shown with the choices; only one can be chosen. If you want more |
| 3507 | | than one, redo this command. After selecting a phase, a dialog box |
| 3508 | | is shown with the proposed phase name. You can change it if desired. |
| 3509 | | <DT>PDB file |
| 3510 | | <DD>This reads the macromolecular phase information from a |
| 3511 | | Protein Data Base file (name.PDB or name.ENT). The file name is |
| 3512 | | found in a directory dialog; you can change directories as |
| 3513 | | needed. Only .PDB (or .pdb) or .ENT (or .ent) file names are |
| 3514 | | shown. Be careful that the space group symbol on the ‘CRYST1’ record |
| 3515 | | in the PDB file follows the GSAS-II conventions (e.g. with spaces |
| 3516 | | between axial fields). A dialog box is shown with the proposed phase |
| 3517 | | name. You can change it if desired. |
| 3518 | | <DT>CIF file |
| 3519 | | <DD>This reads one phase from a Crystallographic Information |
| 3520 | | File ({name}.CIF (or .cif). The file name is found in a directory |
| 3521 | | dialog; you can change directories as needed. If the selected file |
| 3522 | | has more than one phase, a dialog is shown with the choices; only |
| 3523 | | one can be chosen. If you want more than one, redo this |
| 3524 | | command. After selecting a phase, a dialog box is shown with the |
| 3525 | | proposed phase name. You can change it if desired. |
| 3526 | | <DT>GSAS-II .gpx file |
| 3527 | | <DD>This reads one phase from a GSAS-II project file |
| 3528 | | ({name}.gpx). The file name is found in a directory dialog; you can |
| 3529 | | change directories as needed. If the selected file has more |
| 3530 | | than one phase, a dialog is shown with the choices; If you |
| 3531 | | want more than one, redo this command. |
| 3532 | | After selecting a phase, a dialog box is shown with the |
| 3533 | | proposed phase name. You can change it if desired. |
| 3534 | | <DT>guess format from file |
| 3535 | | <DD>This attempts to read one phase from a file trying the |
| 3536 | | formats as described above. On occasion, this command may |
| 3537 | | not succeed in correctly determining a file format. If it fails, |
| 3538 | | retry by selecting the correct format from the list. |
| 3539 | | </DL> |
| 3540 | | <DT><b>Powder Data</b> |
| 3541 | | <DD>Reads a powder diffraction data set in a variety of |
| 3542 | | formats. Results are placed in the GSAS-II data tree as ‘PWDR file |
| 3543 | | name'. Information needed for processing a powder diffraction data |
| 3544 | | set, such as data type, calibration constants (such as wavelength) |
| 3545 | | and default profile parameters are read from a separate file, either |
| 3546 | | a (old) GSAS instrument parameter file (usually .prm, .ins or .inst |
| 3547 | | extension) or a new GSAS-II .instparm file. |
| 3548 | | <P>Note that it is possible to apply corrections to the 2-theta, |
| 3549 | | intensity or weight values by adding a Python command(s) to |
| 3550 | | the instrument (.instprm) parameter with a variable named |
| 3551 | | CorrectionCode. See the <tt>CorrectionCode.instprm.sample</tt> file |
| 3552 | | provided in the GSAS-II source directory for an example of how this |
| 3553 | | is done. |
| 3554 | | <DL> |
| 3555 | | <DT>CIF file |
| 3556 | | <DD>This reads one powder pattern (histogram) from a Crystallographic |
| 3557 | | Information File ({name}.CIF). The file name is found in a directory |
| 3558 | | dialog; you can change directories as needed. Only one .cif can be |
| 3559 | | chosen. If you want more than one, redo this command. |
| 3560 | | <DT>GSAS-II .gpx file |
| 3561 | | <DD>This reads powder patterns from a previously created |
| 3562 | | GSAS-II <span class=SpellE>gpx</span> project file. If the selected |
| 3563 | | file has more than one powder pattern, a dialog is shown with the |
| 3564 | | choices; one or more can be selected. It will ask for an appropriate |
| 3565 | | instrument parameter file to go with the selected powder data sets. |
| 3566 | | <DT>GSAS .fxye files |
| 3567 | | <DD>This reads powder patterns (histograms) from the defined GSAS |
| 3568 | | format powder data files. GSAS file types STD, ESD, FXY and FXYE are |
| 3569 | | recognized. Neutron TOF data with a ‘TIME-MAP’ are also |
| 3570 | | recognized. The file names are found in a directory dialog; you can |
| 3571 | | change directories as needed. If the selected files have more than |
| 3572 | | one powder pattern, a dialog is shown with the choice(s). |
| 3573 | | <DT>TOPAS .xye files. |
| 3574 | | <DD>This format is a simple 3-column (2-theta, intensity |
| 3575 | | & sig) text file. The file names are found in a directory |
| 3576 | | dialog; you can change directories as needed. |
| 3577 | | <DT>guess format from file |
| 3578 | | <DD>This attempts to read one data set from a file trying the |
| 3579 | | formats as described above. On occasion, this command may |
| 3580 | | not succeed in correctly determining a file format. If it fails, |
| 3581 | | retry by selecting the correct format from the list. |
| 3582 | | </DL> |
| 3583 | | <DT><b>Structure Factor</b> |
| 3584 | | <DD>Reads single crystal input from a variety of file |
| 3585 | | types. Results are placed in the GSAS-II data tree as ‘HKLF file name’ |
| 3586 | | <DL> |
| 3587 | | <DT>F**2 HKL file |
| 3588 | | <DD>This reads squared structure factors (as F**2) and sig(F**2) from a |
| 3589 | | SHELX format .hkl file. The file names are found in a |
| 3590 | | directory dialog; you can change directories as needed. You must |
| 3591 | | know the file contains structure factors (as F**2) as the file |
| 3592 | | itself has no internal indication of this. |
| 3593 | | <DT>F HKL file |
| 3594 | | <DD>This reads structure factors (as F) and sig(F) from a |
| 3595 | | SHELX format .hkl file. The file names are found in a |
| 3596 | | directory dialog; you can change directories as needed. You must |
| 3597 | | know the file contains structure factors (as F values) as the file |
| 3598 | | itself has no internal indication of this. |
| 3599 | | <DT>CIF file |
| 3600 | | <DD>This reads structure factors (as F**2 or F) and |
| 3601 | | sig(F**2 or F) from a .CIF (or .cif) or .FCF (or .fcf) format |
| 3602 | | file. The file names are found in a directory dialog; you can change |
| 3603 | | directories as needed. The internal structure of this file indicates |
| 3604 | | in which form the structure factors are used. |
| 3605 | | <DT>guess format from file |
| 3606 | | <DD>This attempts to read one data set from a file trying the |
| 3607 | | formats as described above. However, since it cannot be |
| 3608 | | determined if SHELX format .hkl contaings F or F**2 values, do not |
| 3609 | | use this command for those files. On occasion, this command may |
| 3610 | | not succeed in correctly determining a file format. If it fails, |
| 3611 | | retry by selecting the correct format from the list. |
| 3612 | | </DL> |
| 3613 | | <DT><b>Small Angle Data</b> |
| 3614 | | <DD>Reads small angle scattering data from files. At present these |
| 3615 | | formats are not documented; See the importer routines (file |
| 3616 | | <tt>.../GSASII/imports/G2sad_xye.py</tt>) for more details. |
| 3617 | | </DL> |
| 3618 | | |
| 3619 | | <LI>Menu <B>Export</B> |
| 3620 | | <P>GSAS-II uses separate routines to write out files with |
| 3621 | | information inside GSAS-II. These routines can be |
| 3622 | | created and customized easily. See the GSAS-II Export Modules |
| 3623 | | section of the <a href=#Programmers><strong>Programmers |
| 3624 | | documentation</strong></a> for more information on this. Since it is |
| 3625 | | easy to support new formats, the documentation below may not list |
| 3626 | | all supported formats. |
| 3627 | | <DL style='margin-left:.2in'> |
| 3628 | | <DT><b>Entire project as</b> |
| 3629 | | <DD>At present the only supported format for a project is a Full CIF |
| 3630 | | file. This brings up a separate window where information such as |
| 3631 | | ranges for bond distances and angles can be selected. |
| 3632 | | <DT><b>Phase as</b> |
| 3633 | | <DD>Phases can be exported in a variety of formats including a |
| 3634 | | simplified CIF file that contains only the unit cell, symmetry and |
| 3635 | | coordinates. |
| 3636 | | <DT><b>Powder data as</b> |
| 3637 | | <DD>Powder data can be exported in number of formats. Note that |
| 3638 | | this menu can also be used to export reflection lists from Rietveld |
| 3639 | | and Pawley fits. |
| 3640 | | <DT><b>Single crystal data as</b> |
| 3641 | | <DD>Single crystal reflection lists can be exported as text files |
| 3642 | | or as a simplified CIF file that contains only structure factors. |
| 3643 | | <DT><b>Image data</b> |
| 3644 | | <DD>This exports selected images as a portable networks graphics format |
| 3645 | | (PNG) file. Alternately, the image controls and masks can be written |
| 3646 | | for selected images. If strain analysis has been performed on |
| 3647 | | images, the results can also be exported here as a spreadsheet |
| 3648 | | (.csv file). |
| 3649 | | <DT><b>Maps as </b> |
| 3650 | | <DD>Fourier maps can be exported here. |
| 3651 | | <DT><b>Export all Peak Lists...</b> |
| 3652 | | <DD>This allows peak lists from selected powder histograms to be written |
| 3653 | | to a simple text file. There will be a heading for each PWDR GSAS-II |
| 3654 | | tree item and columns of values for position, intensity, sigma and |
| 3655 | | gamma follow. |
| 3656 | | <DT><b>Export HKLs</b> |
| 3657 | | <DD>This allows single crystal reflection lists from selected |
| 3658 | | histograms to be written to a file. |
| 3659 | | <DT><b>Export PDF...</b> |
| 3660 | | <DD>This allows computed PDFs peak lists from selected histograms |
| 3661 | | to be written as two simple text files, {name}.gr and {name}.sq, |
| 3662 | | containing g(r) and s(q), respectively as 2 columns of data; a |
| 3663 | | header on each indicated the source file name and the column |
| 3664 | | headings. The file name comes from the PDF entry in the GSAS-II data tree. |
| 3665 | | </DL> |
| 3666 | | </OL> |
| | 3241 | </span></div> |
| | 3242 | |
| | 3243 | <h2><a name="main_menu"><span style='mso-fareast-font-family:"Times New Roman"'>4. |
| | 3244 | Main GSAS-II menu commands</span></a><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h2> |
| | 3245 | |
| | 3246 | <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto; |
| | 3247 | margin-left:.7in;text-indent:-.25in;mso-list:l9 level1 lfo2;tab-stops:list .5in'><![if !supportLists]><span |
| | 3248 | style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span |
| | 3249 | style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span |
| | 3250 | style='mso-fareast-font-family:"Times New Roman"'>Menu <b>File</b> <o:p></o:p></span></p> |
| | 3251 | |
| | 3252 | <p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family: |
| | 3253 | "Times New Roman"'>Open project…</span></b><span style='mso-fareast-font-family: |
| | 3254 | "Times New Roman"'> <o:p></o:p></span></p> |
| | 3255 | |
| | 3256 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3257 | "Times New Roman"'>Open a previously saved GSAS-II project file ({project}.gpx). |
| | 3258 | If you currently have a project file open, you are asked if it is OK to |
| | 3259 | overwrite it; Cancel will cancel the read process. <o:p></o:p></span></p> |
| | 3260 | |
| | 3261 | <p style='margin-left:.5in'>Note that as files are saved, copies of the |
| | 3262 | previous version are saved as backup files, named as {project}.bak{<i>i</i>}.gpx, |
| | 3263 | where <i>i</i> starts as 0 and is increased after each save operation. NB: you |
| | 3264 | may open a backup .gpx file (e.g. name.bak3.gpx) to return to a previous |
| | 3265 | version of your project, but if you do so, it is best to immediately use the <b'>Save |
| | 3266 | As... menu command (you may wish to use name.gpx to overwrite the current |
| | 3267 | version or select a new name.) If you forget specify a project name, then |
| | 3268 | name.bak3 will be considered the project name and backups will then be named |
| | 3269 | name.bak3.bak0.gpx, etc.</p> |
| | 3270 | |
| | 3271 | <p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family: |
| | 3272 | "Times New Roman"'>Save project</span></b><span style='mso-fareast-font-family: |
| | 3273 | "Times New Roman"'> <o:p></o:p></span></p> |
| | 3274 | |
| | 3275 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3276 | "Times New Roman"'>Save the current project. If this is a new project that has |
| | 3277 | not yet been saved, you will be prompted for a new name in a file dialog (you |
| | 3278 | may optionally change the directory in that dialog). If the file exists, you |
| | 3279 | will be asked if it is OK to overwrite it. Once a file name has been used to |
| | 3280 | read or save a project, the name is shown after ‘Loaded Data:’ in the first |
| | 3281 | item in the data tree. <o:p></o:p></span></p> |
| | 3282 | |
| | 3283 | <p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family: |
| | 3284 | "Times New Roman"'>Save Project as...</span></b><span style='mso-fareast-font-family: |
| | 3285 | "Times New Roman"'> <o:p></o:p></span></p> |
| | 3286 | |
| | 3287 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3288 | "Times New Roman"'>Save the current project in a specified project file. You |
| | 3289 | will be prompted for a new name in a file dialog (you may optionally change the |
| | 3290 | directory in that dialog). If the file exists, you will be asked if it is OK to |
| | 3291 | overwrite it. <o:p></o:p></span></p> |
| | 3292 | |
| | 3293 | <p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family: |
| | 3294 | "Times New Roman"'>New Project</span></b><span style='mso-fareast-font-family: |
| | 3295 | "Times New Roman"'> <o:p></o:p></span></p> |
| | 3296 | |
| | 3297 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3298 | "Times New Roman"'>Discards any changes made to the current project since the |
| | 3299 | last save and creates a new empty project. <o:p></o:p></span></p> |
| | 3300 | |
| | 3301 | <p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family: |
| | 3302 | "Times New Roman"'>Preferences</span></b><span style='mso-fareast-font-family: |
| | 3303 | "Times New Roman"'> <o:p></o:p></span></p> |
| | 3304 | |
| | 3305 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3306 | "Times New Roman"'>Provides access to GSAS-II configuration settings, as |
| | 3307 | described in the <a href="#Preferences">Configuration Variables</a> section. <o:p></o:p></span></p> |
| | 3308 | |
| | 3309 | <p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family: |
| | 3310 | "Times New Roman"'>Quit</span></b><span style='mso-fareast-font-family:"Times New Roman"'> |
| | 3311 | <o:p></o:p></span></p> |
| | 3312 | |
| | 3313 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3314 | "Times New Roman"'>Exit the GSAS-II program. Discards any changes made to the |
| | 3315 | current project since the last save. You can also exit GSAS-II by pressing the |
| | 3316 | red X in the upper right (Windows) or left (Mac). <o:p></o:p></span></p> |
| | 3317 | |
| | 3318 | <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto; |
| | 3319 | margin-left:.7in;text-indent:-.25in;mso-list:l9 level1 lfo2;tab-stops:list .5in'><![if !supportLists]><span |
| | 3320 | style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span |
| | 3321 | style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span |
| | 3322 | style='mso-fareast-font-family:"Times New Roman"'>Menu <b>Data</b> <o:p></o:p></span></p> |
| | 3323 | |
| | 3324 | <p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family: |
| | 3325 | "Times New Roman"'>Read Powder Pattern Peaks…</span></b><span style='mso-fareast-font-family: |
| | 3326 | "Times New Roman"'> <o:p></o:p></span></p> |
| | 3327 | |
| | 3328 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3329 | "Times New Roman"'>Read in a list of powder pattern peak positions as either a |
| | 3330 | d-spacing table or a set of 2theta positions; these can be used in GSAS-II |
| | 3331 | powder pattern indexing. <o:p></o:p></span></p> |
| | 3332 | |
| | 3333 | <p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family: |
| | 3334 | "Times New Roman"'>Sum powder data</span></b><span style='mso-fareast-font-family: |
| | 3335 | "Times New Roman"'> <o:p></o:p></span></p> |
| | 3336 | |
| | 3337 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3338 | "Times New Roman"'>Form the sum of previously read powder patterns; each with a |
| | 3339 | multiplier. Can be used to accumulate data, subtract background or empty |
| | 3340 | container patterns, etc. Patterns used to form the sum must be of identical |
| | 3341 | range and step size. Result is a new PWDR entry in the GSAS-II data tree. <o:p></o:p></span></p> |
| | 3342 | |
| | 3343 | <p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family: |
| | 3344 | "Times New Roman"'>Sum image data</span></b><span style='mso-fareast-font-family: |
| | 3345 | "Times New Roman"'> <o:p></o:p></span></p> |
| | 3346 | |
| | 3347 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3348 | "Times New Roman"'>Form the sum of previously read 2-D images; each with a |
| | 3349 | multiplier. Can be used to accumulate data, subtract background or empty |
| | 3350 | container patterns, etc. Images used to form the sum must be of identical size |
| | 3351 | and source. Result is a new IMG entry in the GSAS-II data tree, and a GSAS-II |
| | 3352 | image file is written for future use. <o:p></o:p></span></p> |
| | 3353 | |
| | 3354 | <p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family: |
| | 3355 | "Times New Roman"'>Add new phase </span></b><span style='mso-fareast-font-family: |
| | 3356 | "Times New Roman"'><o:p></o:p></span></p> |
| | 3357 | |
| | 3358 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3359 | "Times New Roman"'>This begins the creation of a new phase in the data tree |
| | 3360 | (under Phases). You are first prompted in a dialog box for a name to be |
| | 3361 | assigned to the new phase. Then the Phase/<a href="#General">General</a> tab is |
| | 3362 | opened for this phase, where you should first select the phase type, the enter |
| | 3363 | the space group symbol and then the lattice parameters. <br> |
| | 3364 | Note that nonstandard space group symbols are permitted; space group names must |
| | 3365 | have spaces between the axial fields (e.g. use ‘P n a 21’ not ‘Pna21’). <o:p></o:p></span></p> |
| | 3366 | |
| | 3367 | <p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family: |
| | 3368 | "Times New Roman"'>Delete phase</span></b><span style='mso-fareast-font-family: |
| | 3369 | "Times New Roman"'> <o:p></o:p></span></p> |
| | 3370 | |
| | 3371 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3372 | "Times New Roman"'>This will remove a phase from the data tree. A dialog box |
| | 3373 | will present the list of phases; pick one (or more) to delete. <o:p></o:p></span></p> |
| | 3374 | |
| | 3375 | <p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family: |
| | 3376 | "Times New Roman"'>Rename tree item</span></b><span style='mso-fareast-font-family: |
| | 3377 | "Times New Roman"'> <o:p></o:p></span></p> |
| | 3378 | |
| | 3379 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3380 | "Times New Roman"'>Rename a histogram entry. This should only be done before |
| | 3381 | the histogram is used in any phases: e.g. only rename data immediately after |
| | 3382 | reading. <o:p></o:p></span></p> |
| | 3383 | |
| | 3384 | <p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family: |
| | 3385 | "Times New Roman"'>Delete tree item</span></b><span style='mso-fareast-font-family: |
| | 3386 | "Times New Roman"'> <o:p></o:p></span></p> |
| | 3387 | |
| | 3388 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3389 | "Times New Roman"'>This will remove an item from the data tree. A dialog box |
| | 3390 | with a list of choices for histograms is presented. Be sure to remove a |
| | 3391 | histograms from all phases before deleting it from the tree. <o:p></o:p></span></p> |
| | 3392 | |
| | 3393 | <p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family: |
| | 3394 | "Times New Roman"'>Expand tree item</span></b><span style='mso-fareast-font-family: |
| | 3395 | "Times New Roman"'> <o:p></o:p></span></p> |
| | 3396 | |
| | 3397 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3398 | "Times New Roman"'>This will show child entries for specified type of items |
| | 3399 | (Images, Powder patterns, etc.)<o:p></o:p></span></p> |
| | 3400 | |
| | 3401 | <p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family: |
| | 3402 | "Times New Roman"'>Move tree item</span></b><span style='mso-fareast-font-family: |
| | 3403 | "Times New Roman"'> <o:p></o:p></span></p> |
| | 3404 | |
| | 3405 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3406 | "Times New Roman"'>Move classes of Tree items around in the tree. Individual |
| | 3407 | top-level tree items can be moved using the left mouse button. <o:p></o:p></span></p> |
| | 3408 | |
| | 3409 | <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto; |
| | 3410 | margin-left:.7in;text-indent:-.25in;mso-list:l9 level1 lfo2;tab-stops:list .5in'><![if !supportLists]><span |
| | 3411 | style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span |
| | 3412 | style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span |
| | 3413 | style='mso-fareast-font-family:"Times New Roman"'>Menu <a name="Calculate_menu"><b>Calculate</b></a> |
| | 3414 | <o:p></o:p></span></p> |
| | 3415 | |
| | 3416 | <p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family: |
| | 3417 | "Times New Roman"'>Setup PDFs</span></b><span style='mso-fareast-font-family: |
| | 3418 | "Times New Roman"'> <o:p></o:p></span></p> |
| | 3419 | |
| | 3420 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3421 | "Times New Roman"'>This creates the pair distribution function (PDF) controls |
| | 3422 | for each powder pattern selected in the dialog box, but does not compute the |
| | 3423 | PDF, which must be done from <b><a href="#PDF">PDF tree entries</a></b>. See <b><a |
| | 3424 | href="#PDF_Controls">PDF Controls</a></b> for information on the PDF input. <o:p></o:p></span></p> |
| | 3425 | |
| | 3426 | <p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family: |
| | 3427 | "Times New Roman"'>View LS parms</span></b><span style='mso-fareast-font-family: |
| | 3428 | "Times New Roman"'> <o:p></o:p></span></p> |
| | 3429 | |
| | 3430 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3431 | "Times New Roman"'>This shows a dialog box with all the parameters for your |
| | 3432 | project; those to be refined are flagged ‘True’, otherwise ‘False’. Blanks |
| | 3433 | indicate parameters that are not refinable. The total number of refined parameters |
| | 3434 | is also shown at the top of the list. The value of each parameter is also |
| | 3435 | given. The parameter names are of the form ‘p:h:name:id’ where ‘p’ is the phase |
| | 3436 | index, ‘h’ is the histogram index and ‘id’ is the item index (if needed). |
| | 3437 | Indexes all begin with ‘0’ (zero). <o:p></o:p></span></p> |
| | 3438 | |
| | 3439 | <p style='margin-left:.5in'>Note that for atom positions, the coordinate values |
| | 3440 | (named as ‘p::A<i>w</i>:n’, where p is the phase number, n is the atom number |
| | 3441 | and <i>w</i> is x, y or z) is not a refinable parameter, but the shift in the |
| | 3442 | value is. The refined parameters are ‘p::A<i>w</i>:n’. The reason this is done |
| | 3443 | is that by treating an atom position as x+dx,y+dy,z+dz where the “d” values |
| | 3444 | indicate shifts from the starting position and the shifts are refined rather |
| | 3445 | than the x,y, or z values is that this simplifies symmetry constraints. As an example, |
| | 3446 | suppose we have an atom on a symmetry constrained site, x,1/2-x,z. The process |
| | 3447 | needed to define this constraint, so that if x moves positively y has to move |
| | 3448 | negatively by the same amount would be messy. With refinement of shifts, all we |
| | 3449 | need to do is constrain dy (‘0::dAy:n’) to be equal to -dx (-1*‘0::dAx:n’). </p> |
| | 3450 | |
| | 3451 | <p style='margin-left:.5in'>Press the window exit button to exit this dialog |
| | 3452 | box. </p> |
| | 3453 | |
| | 3454 | <p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family: |
| | 3455 | "Times New Roman"'>Refine</span></b><span style='mso-fareast-font-family:"Times New Roman"'> |
| | 3456 | <o:p></o:p></span></p> |
| | 3457 | |
| | 3458 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3459 | "Times New Roman"'>This performs the refinement (Pawley/Rietveld or single |
| | 3460 | crystal) according to the controls set in the <b><a href="#Controls">Controls</a></b> |
| | 3461 | data tree item. <o:p></o:p></span></p> |
| | 3462 | |
| | 3463 | <p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family: |
| | 3464 | "Times New Roman"'>Sequential refine</span></b><span style='mso-fareast-font-family: |
| | 3465 | "Times New Roman"'> <o:p></o:p></span></p> |
| | 3466 | |
| | 3467 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3468 | "Times New Roman"'>This starts a sequential refinement with the data sets |
| | 3469 | selected in the <b><a href="#Controls">Controls</a></b> data tree item. <o:p></o:p></span></p> |
| | 3470 | |
| | 3471 | <ol start=4 type=1> |
| | 3472 | <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto; |
| | 3473 | mso-list:l9 level1 lfo2;tab-stops:list .5in'><span style='mso-fareast-font-family: |
| | 3474 | "Times New Roman"'>Menu <b>Import</b> <o:p></o:p></span></li> |
| | 3475 | </ol> |
| | 3476 | |
| | 3477 | <p style='margin-left:.5in'>GSAS-II uses separate routines to read in |
| | 3478 | information from external files that can be created and customized easily. See |
| | 3479 | the GSAS-II Import Modules section of the <a href="#Programmers"><strong>Programmers |
| | 3480 | documentation</strong></a> for more information on this. Since it is easy to |
| | 3481 | support new formats, the documentation below may not list all supported |
| | 3482 | formats. </p> |
| | 3483 | |
| | 3484 | <p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family: |
| | 3485 | "Times New Roman"'>Image</span></b><span style='mso-fareast-font-family:"Times New Roman"'> |
| | 3486 | <o:p></o:p></span></p> |
| | 3487 | |
| | 3488 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3489 | "Times New Roman"'>Read in 2-D powder diffraction images (multiple patterns can |
| | 3490 | be selected). A sub menu appears with choices for import of data. Each entry |
| | 3491 | when selected with the mouse shows further submenus with specific imports that |
| | 3492 | are available. Any of these files can be accessed from a zip file. GSAS-II can |
| | 3493 | read many different image file formats including MAR345 files, Quantum ADSC |
| | 3494 | files, and tiff files from Perkin-Elmer, Pilatus, and GE. Although many of |
| | 3495 | these formats have data fields that should contain relevant information for the |
| | 3496 | exposure (e.g. wavelength), these are rarely filled in correctly by the data |
| | 3497 | acquisition software. Thus, you should have separately noted this information |
| | 3498 | as it will be needed <o:p></o:p></span></p> |
| | 3499 | |
| | 3500 | <p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family: |
| | 3501 | "Times New Roman"'>Phase</span></b><span style='mso-fareast-font-family:"Times New Roman"'> |
| | 3502 | <o:p></o:p></span></p> |
| | 3503 | |
| | 3504 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3505 | "Times New Roman"'>Creates a new phase by reading unit cell/symmetry/atom |
| | 3506 | coordinate information. GSAS-II can read information from a number of different |
| | 3507 | format files including: <o:p></o:p></span></p> |
| | 3508 | |
| | 3509 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3510 | "Times New Roman"'>GSAS .EXP <o:p></o:p></span></p> |
| | 3511 | |
| | 3512 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3513 | "Times New Roman"'>This reads one phase from a (old) GSAS experiment file |
| | 3514 | (name.EXP). The file name is found in a directory dialog; you can change |
| | 3515 | directories as needed. Only .EXP (or .exp) file names are shown. If the |
| | 3516 | selected file has more than one phase, a dialog is shown with the choices; only |
| | 3517 | one can be chosen. If you want more than one, redo this command. After |
| | 3518 | selecting a phase, a dialog box is shown with the proposed phase name. You can |
| | 3519 | change it if desired. <o:p></o:p></span></p> |
| | 3520 | |
| | 3521 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3522 | "Times New Roman"'>PDB file <o:p></o:p></span></p> |
| | 3523 | |
| | 3524 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3525 | "Times New Roman"'>This reads the macromolecular phase information from a |
| | 3526 | Protein Data Base file (name.PDB or name.ENT). The file name is found in a |
| | 3527 | directory dialog; you can change directories as needed. Only .PDB (or .pdb) or |
| | 3528 | .ENT (or .ent) file names are shown. Be careful that the space group symbol on |
| | 3529 | the ‘CRYST1’ record in the PDB file follows the GSAS-II conventions (e.g. with |
| | 3530 | spaces between axial fields). A dialog box is shown with the proposed phase |
| | 3531 | name. You can change it if desired. <o:p></o:p></span></p> |
| | 3532 | |
| | 3533 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3534 | "Times New Roman"'>CIF file <o:p></o:p></span></p> |
| | 3535 | |
| | 3536 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3537 | "Times New Roman"'>This reads one phase from a Crystallographic Information |
| | 3538 | File ({name}.CIF (or .cif). The file name is found in a directory dialog; you |
| | 3539 | can change directories as needed. If the selected file has more than one phase, |
| | 3540 | a dialog is shown with the choices; only one can be chosen. If you want more |
| | 3541 | than one, redo this command. After selecting a phase, a dialog box is shown |
| | 3542 | with the proposed phase name. You can change it if desired. <o:p></o:p></span></p> |
| | 3543 | |
| | 3544 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3545 | "Times New Roman"'>GSAS-II .gpx file <o:p></o:p></span></p> |
| | 3546 | |
| | 3547 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3548 | "Times New Roman"'>This reads one phase from a GSAS-II project file |
| | 3549 | ({name}.gpx). The file name is found in a directory dialog; you can change |
| | 3550 | directories as needed. If the selected file has more than one phase, a dialog |
| | 3551 | is shown with the choices; If you want more than one, redo this command. After |
| | 3552 | selecting a phase, a dialog box is shown with the proposed phase name. You can |
| | 3553 | change it if desired. <o:p></o:p></span></p> |
| | 3554 | |
| | 3555 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3556 | "Times New Roman"'>guess format from file <o:p></o:p></span></p> |
| | 3557 | |
| | 3558 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3559 | "Times New Roman"'>This attempts to read one phase from a file trying the |
| | 3560 | formats as described above. On occasion, this command may not succeed in |
| | 3561 | correctly determining a file format. If it fails, retry by selecting the |
| | 3562 | correct format from the list. <o:p></o:p></span></p> |
| | 3563 | |
| | 3564 | <p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family: |
| | 3565 | "Times New Roman"'>Powder Data</span></b><span style='mso-fareast-font-family: |
| | 3566 | "Times New Roman"'> <o:p></o:p></span></p> |
| | 3567 | |
| | 3568 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3569 | "Times New Roman"'>Reads a powder diffraction data set in a variety of formats. |
| | 3570 | Results are placed in the GSAS-II data tree as ‘PWDR file name'. Information |
| | 3571 | needed for processing a powder diffraction data set, such as data type, |
| | 3572 | calibration constants (such as wavelength) and default profile parameters are |
| | 3573 | read from a separate file, either a (old) GSAS instrument parameter file |
| | 3574 | (usually .prm, .ins or .inst extension) or a new GSAS-II .instparm file. <o:p></o:p></span></p> |
| | 3575 | |
| | 3576 | <p style='margin-left:.5in'>Note that it is possible to apply corrections to |
| | 3577 | the 2-theta, intensity or weight values by adding a Python command(s) to the |
| | 3578 | instrument (.instprm) parameter with a variable named CorrectionCode. See the <tt><span |
| | 3579 | style='font-size:10.0pt'>CorrectionCode.instprm.sample</span></tt> file |
| | 3580 | provided in the GSAS-II source directory for an example of how this is done. </p> |
| | 3581 | |
| | 3582 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3583 | "Times New Roman"'>CIF file <o:p></o:p></span></p> |
| | 3584 | |
| | 3585 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3586 | "Times New Roman"'>This reads one powder pattern (histogram) from a |
| | 3587 | Crystallographic Information File ({name}.CIF). The file name is found in a |
| | 3588 | directory dialog; you can change directories as needed. Only one .cif can be |
| | 3589 | chosen. If you want more than one, redo this command. <o:p></o:p></span></p> |
| | 3590 | |
| | 3591 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3592 | "Times New Roman"'>GSAS-II .gpx file <o:p></o:p></span></p> |
| | 3593 | |
| | 3594 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3595 | "Times New Roman"'>This reads powder patterns from a previously created GSAS-II |
| | 3596 | gpx project file. If the selected file has more than one powder pattern, a |
| | 3597 | dialog is shown with the choices; one or more can be selected. It will ask for |
| | 3598 | an appropriate instrument parameter file to go with the selected powder data |
| | 3599 | sets. <o:p></o:p></span></p> |
| | 3600 | |
| | 3601 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3602 | "Times New Roman"'>GSAS .fxye files <o:p></o:p></span></p> |
| | 3603 | |
| | 3604 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3605 | "Times New Roman"'>This reads powder patterns (histograms) from the defined |
| | 3606 | GSAS format powder data files. GSAS file types STD, ESD, FXY and FXYE are |
| | 3607 | recognized. Neutron TOF data with a ‘TIME-MAP’ are also recognized. The file |
| | 3608 | names are found in a directory dialog; you can change directories as needed. If |
| | 3609 | the selected files have more than one powder pattern, a dialog is shown with |
| | 3610 | the choice(s). <o:p></o:p></span></p> |
| | 3611 | |
| | 3612 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3613 | "Times New Roman"'>TOPAS .xye files. <o:p></o:p></span></p> |
| | 3614 | |
| | 3615 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3616 | "Times New Roman"'>This format is a simple 3-column (2-theta, intensity & |
| | 3617 | sig) text file. The file names are found in a directory dialog; you can change |
| | 3618 | directories as needed. <o:p></o:p></span></p> |
| | 3619 | |
| | 3620 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3621 | "Times New Roman"'>guess format from file <o:p></o:p></span></p> |
| | 3622 | |
| | 3623 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3624 | "Times New Roman"'>This attempts to read one data set from a file trying the |
| | 3625 | formats as described above. On occasion, this command may not succeed in |
| | 3626 | correctly determining a file format. If it fails, retry by selecting the |
| | 3627 | correct format from the list. <o:p></o:p></span></p> |
| | 3628 | |
| | 3629 | <p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family: |
| | 3630 | "Times New Roman"'>Structure Factor</span></b><span style='mso-fareast-font-family: |
| | 3631 | "Times New Roman"'> <o:p></o:p></span></p> |
| | 3632 | |
| | 3633 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3634 | "Times New Roman"'>Reads single crystal input from a variety of file types. |
| | 3635 | Results are placed in the GSAS-II data tree as ‘HKLF file name’ <o:p></o:p></span></p> |
| | 3636 | |
| | 3637 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3638 | "Times New Roman"'>F**2 HKL file <o:p></o:p></span></p> |
| | 3639 | |
| | 3640 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3641 | "Times New Roman"'>This reads squared structure factors (as F**2) and sig(F**2) |
| | 3642 | from a SHELX format .hkl file. The file names are found in a directory dialog; |
| | 3643 | you can change directories as needed. You must know the file contains structure |
| | 3644 | factors (as F**2) as the file itself has no internal indication of this. <o:p></o:p></span></p> |
| | 3645 | |
| | 3646 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3647 | "Times New Roman"'>F HKL file <o:p></o:p></span></p> |
| | 3648 | |
| | 3649 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3650 | "Times New Roman"'>This reads structure factors (as F) and sig(F) from a SHELX |
| | 3651 | format .hkl file. The file names are found in a directory dialog; you can |
| | 3652 | change directories as needed. You must know the file contains structure factors |
| | 3653 | (as F values) as the file itself has no internal indication of this. <o:p></o:p></span></p> |
| | 3654 | |
| | 3655 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3656 | "Times New Roman"'>CIF file <o:p></o:p></span></p> |
| | 3657 | |
| | 3658 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3659 | "Times New Roman"'>This reads structure factors (as F**2 or F) and sig(F**2 or |
| | 3660 | F) from a .CIF (or .cif) or .FCF (or .fcf) format file. The file names are |
| | 3661 | found in a directory dialog; you can change directories as needed. The internal |
| | 3662 | structure of this file indicates in which form the structure factors are used. <o:p></o:p></span></p> |
| | 3663 | |
| | 3664 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3665 | "Times New Roman"'>guess format from file <o:p></o:p></span></p> |
| | 3666 | |
| | 3667 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3668 | "Times New Roman"'>This attempts to read one data set from a file trying the |
| | 3669 | formats as described above. However, since it cannot be determined if SHELX |
| | 3670 | format .hkl contaings F or F**2 values, do not use this command for those |
| | 3671 | files. On occasion, this command may not succeed in correctly determining a |
| | 3672 | file format. If it fails, retry by selecting the correct format from the list. <o:p></o:p></span></p> |
| | 3673 | |
| | 3674 | <p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family: |
| | 3675 | "Times New Roman"'>Small Angle Data</span></b><span style='mso-fareast-font-family: |
| | 3676 | "Times New Roman"'> <o:p></o:p></span></p> |
| | 3677 | |
| | 3678 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3679 | "Times New Roman"'>Reads small angle scattering data from files. At present |
| | 3680 | these formats are not documented; See the importer routines (file </span><tt><span |
| | 3681 | style='font-size:10.0pt'>.../GSASII/imports/G2sad_xye.py</span></tt><span |
| | 3682 | style='mso-fareast-font-family:"Times New Roman"'>) for more details. <o:p></o:p></span></p> |
| | 3683 | |
| | 3684 | <ol start=5 type=1> |
| | 3685 | <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto; |
| | 3686 | mso-list:l9 level1 lfo2;tab-stops:list .5in'><span style='mso-fareast-font-family: |
| | 3687 | "Times New Roman"'>Menu <b>Export</b> <o:p></o:p></span></li> |
| | 3688 | </ol> |
| | 3689 | |
| | 3690 | <p style='margin-left:.5in'>GSAS-II uses separate routines to write out files |
| | 3691 | with information inside GSAS-II. These routines can be created and customized |
| | 3692 | easily. See the GSAS-II Export Modules section of the <a href="#Programmers"><strong>Programmers |
| | 3693 | documentation</strong></a> for more information on this. Since it is easy to |
| | 3694 | support new formats, the documentation below may not list all supported |
| | 3695 | formats. </p> |
| | 3696 | |
| | 3697 | <p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family: |
| | 3698 | "Times New Roman"'>Entire project as</span></b><span style='mso-fareast-font-family: |
| | 3699 | "Times New Roman"'> <o:p></o:p></span></p> |
| | 3700 | |
| | 3701 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3702 | "Times New Roman"'>At present the only supported format for a project is a Full |
| | 3703 | CIF file. This brings up a separate window where information such as ranges for |
| | 3704 | bond distances and angles can be selected. <o:p></o:p></span></p> |
| | 3705 | |
| | 3706 | <p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family: |
| | 3707 | "Times New Roman"'>Phase as</span></b><span style='mso-fareast-font-family: |
| | 3708 | "Times New Roman"'> <o:p></o:p></span></p> |
| | 3709 | |
| | 3710 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3711 | "Times New Roman"'>Phases can be exported in a variety of formats including a |
| | 3712 | simplified CIF file that contains only the unit cell, symmetry and coordinates. |
| | 3713 | <o:p></o:p></span></p> |
| | 3714 | |
| | 3715 | <p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family: |
| | 3716 | "Times New Roman"'>Powder data as</span></b><span style='mso-fareast-font-family: |
| | 3717 | "Times New Roman"'> <o:p></o:p></span></p> |
| | 3718 | |
| | 3719 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3720 | "Times New Roman"'>Powder data can be exported in number of formats. Note that |
| | 3721 | this menu can also be used to export reflection lists from Rietveld and Pawley |
| | 3722 | fits. <o:p></o:p></span></p> |
| | 3723 | |
| | 3724 | <p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family: |
| | 3725 | "Times New Roman"'>Single crystal data as</span></b><span style='mso-fareast-font-family: |
| | 3726 | "Times New Roman"'> <o:p></o:p></span></p> |
| | 3727 | |
| | 3728 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3729 | "Times New Roman"'>Single crystal reflection lists can be exported as text |
| | 3730 | files or as a simplified CIF file that contains only structure factors. <o:p></o:p></span></p> |
| | 3731 | |
| | 3732 | <p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family: |
| | 3733 | "Times New Roman"'>Image data</span></b><span style='mso-fareast-font-family: |
| | 3734 | "Times New Roman"'> <o:p></o:p></span></p> |
| | 3735 | |
| | 3736 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3737 | "Times New Roman"'>This exports selected images as a portable networks graphics |
| | 3738 | format (PNG) file. Alternately, the image controls and masks can be written for |
| | 3739 | selected images. If strain analysis has been performed on images, the results |
| | 3740 | can also be exported here as a spreadsheet (.csv file). <o:p></o:p></span></p> |
| | 3741 | |
| | 3742 | <p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family: |
| | 3743 | "Times New Roman"'>Maps as </span></b><span style='mso-fareast-font-family: |
| | 3744 | "Times New Roman"'><o:p></o:p></span></p> |
| | 3745 | |
| | 3746 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3747 | "Times New Roman"'>Fourier maps can be exported here. <o:p></o:p></span></p> |
| | 3748 | |
| | 3749 | <p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family: |
| | 3750 | "Times New Roman"'>Export all Peak Lists...</span></b><span style='mso-fareast-font-family: |
| | 3751 | "Times New Roman"'> <o:p></o:p></span></p> |
| | 3752 | |
| | 3753 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3754 | "Times New Roman"'>This allows peak lists from selected powder histograms to be |
| | 3755 | written to a simple text file. There will be a heading for each PWDR GSAS-II |
| | 3756 | tree item and columns of values for position, intensity, sigma and gamma |
| | 3757 | follow. <o:p></o:p></span></p> |
| | 3758 | |
| | 3759 | <p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family: |
| | 3760 | "Times New Roman"'>Export HKLs</span></b><span style='mso-fareast-font-family: |
| | 3761 | "Times New Roman"'> <o:p></o:p></span></p> |
| | 3762 | |
| | 3763 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3764 | "Times New Roman"'>This allows single crystal reflection lists from selected |
| | 3765 | histograms to be written to a file. <o:p></o:p></span></p> |
| | 3766 | |
| | 3767 | <p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family: |
| | 3768 | "Times New Roman"'>Export PDF...</span></b><span style='mso-fareast-font-family: |
| | 3769 | "Times New Roman"'> <o:p></o:p></span></p> |
| | 3770 | |
| | 3771 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3772 | "Times New Roman"'>This allows computed PDFs peak lists from selected |
| | 3773 | histograms to be written as two simple text files, {name}.gr and {name}.sq, |
| | 3774 | containing g(r) and s(q), respectively as 2 columns of data; a header on each |
| | 3775 | indicated the source file name and the column headings. The file name comes |
| | 3776 | from the PDF entry in the GSAS-II data tree. <o:p></o:p></span></p> |
| | 3777 | |
| | 3778 | <div class=MsoNormal align=center style='text-align:center'><span |
| | 3779 | style='mso-fareast-font-family:"Times New Roman"'> |
| 3696 | | "Times New Roman"'>This window provides access to the controls that |
| 3697 | | determine how GSAS-II performs minimizations as well as few |
| 3698 | | global parameters for GSAS-II. Note that many other customization |
| 3699 | | settings are set as <A Href=#Preferences>configuration variables</a> |
| 3700 | | in the Preferences menu. (See the |
| 3701 | | <a |
| 3702 | | href="https://gsas-ii.readthedocs.io/en/latest/GSASIIutil.html#module-config_example"> |
| 3703 | | Programmer's documentation</a> for a description of those.) |
| 3704 | | </P> |
| 3705 | | |
| 3706 | | <p style='margin-left:0.75in'><U>Refinement Controls:</u><i> These |
| 3707 | | controls determine how refinements are performed. The first determines |
| 3708 | | the computational engine used to minimize the structure. |
| 3709 | | </i></p> |
| 3710 | | |
| 3711 | | <A name="RefineType"></A> |
| 3712 | | <DL style='margin-left:1.0in'> |
| 3713 | | <DT><B>Refinement type</B></DT> |
| 3714 | | <DD>This determines how refinements are performed. The choices |
| 3715 | | are:</DD> |
| 3716 | | <UL style='margin-left:0.25in'> |
| 3717 | | <LI><U>analytic Hessian</U>: This is the default option and is usually |
| 3718 | | the most useful. It uses a custom-developed least-squares |
| 3719 | | minimizer that uses singular-value decomposition (SVD) to reduce the |
| 3720 | | errors caused by correlated variables and the |
| 3721 | | Levenberg-Marquardt algorithm to up-weight diagonal |
| 3722 | | Hessian terms when refinements fail to lower χ<sup>2</sup>. |
| 3723 | | <LI><u>analytic Jacobian</u>: This uses a numpy-provided <I>leastsq</I> |
| 3724 | | minimizer, which not applicable for |
| 3725 | | problem with a large number of histograms as it requires |
| 3726 | | much more memory than the Hessian routines. This because it |
| 3727 | | creates a Jacobian matrix that is shaped N x M (N parameters x M |
| 3728 | | observations) while the Hessian methods create a Jacobian matrix |
| 3729 | | only each histogram. |
| 3730 | | <LI><u>numeric</u>: This also uses the numpy <I>leastsq</I> |
| 3731 | | minimizer, and is also not applicable for larger |
| 3732 | | problems. Unlike, the "analytic Jacobian", numerical derivatives |
| 3733 | | are computed rather than use the analytical derivatives |
| 3734 | | that are coded directly into GSAS-II. This will be slower than |
| 3735 | | the analytical derivatives and will is often less accurate which |
| 3736 | | results in slower convergence. It is |
| 3737 | | typically used for code development to check the accuracy of the |
| 3738 | | analytical derivative formulations. |
| 3739 | | <LI><u>Hessian SVD</u>: This is very similar to <U>analytic |
| 3740 | | Hessian</U> but does not include the Levenberg-Marquardt |
| 3741 | | algorithm. It can be faster, but is more prone to |
| 3742 | | diverge when severe correlation is present. It is possible that |
| 3743 | | it might be better for single-crystal refinements. |
| 3744 | | </UL> |
| 3745 | | <p style='margin-left:0.25in'> |
| 3746 | | Note that the Jacobian refinement tools are the Fortran |
| 3747 | | MINPACK <I>lmdif</I > and <I>lmder</I> algorithms wrapped in python as |
| 3748 | | provided in the <span class=SpellE>Scipy</span> package. The |
| 3749 | | Hessian routines are were developed for GSAS-II based on routines in |
| 3750 | | numpy and scipy and using the material in Numerical Recipes (Press, Flannery, <span class=SpellE>Teulosky</span> |
| 3751 | | & <span class=SpellE>Vetterling</span>) for the <span |
| 3752 | | class=SpellE>Levenberg</span>-Marquardt. |
| 3753 | | The purpose is to </span>minimize |
| 3754 | | the sum of the squares of M<span style='mso-fareast-font-family:"Times New Roman"'> |
| 3755 | | nonlinear functions in N variables by a modification of the <span class=SpellE>Levenberg</span>-Marquardt |
| 3756 | | algorithm. The <span class=SpellE>lmdif</span> and <span class=SpellE>lmder</span> |
| 3757 | | routines were written by </span>Burton S. <span class=SpellE>Garbow</span>, |
| 3758 | | Kenneth E. <span class=SpellE>Hillstrom</span>, Jorge J. More (Argonne National |
| 3759 | | Laboratory, 1980). |
| 3760 | | </p> |
| 3761 | | <DT><B>Min delta-M/M</B></DT> |
| 3762 | | <DD>A refinement will stop when the change in the minimization function |
| 3763 | | (M=Σ[w(Io-Ic)<sup>2</sup>]) |
| 3764 | | is less than this value. The allowed range is 10<sup>-9</sup> to |
| 3765 | | 1.0, with a default of 0.001. A value of |
| 3766 | | 1.0 stops the refinement after a single cycle. Values less than |
| 3767 | | 10<sup>-4</sup> cause refinements to continue even if there is |
| 3768 | | no meaningful improvement. |
| 3769 | | </DD><P></P> |
| 3770 | | <DT><B>Max cycles</B></DT> |
| 3771 | | <DD>This determines the maximum number of refinement cycles that |
| 3772 | | will be performed. This is only available with the "Hessian" minimizers.</DD><P></P> |
| 3773 | | <DT><B>Initial lambda</B></DT> |
| 3774 | | <DD>Note that here λ is the Marquardt coefficient, where a weight of |
| 3775 | | 1+λ is applied to the diagonal elements of the Hessian. When λ is |
| 3776 | | large, this down-weights the significance of the off-diagonal terms in the |
| 3777 | | Hessian. Thus, when λ is large, the refinement is effectively one of |
| 3778 | | steepest-descents, where correlation between variables is |
| 3779 | | ignored. Note that steepest-descents minimization is typically |
| 3780 | | slow and may not always find the local minimum. |
| 3781 | | This is only available with the "analytical Hessian" minimizer. |
| 3782 | | </DD><P></P> |
| 3783 | | <DT><B>SVD zero tolerance</B></DT> |
| 3784 | | <DD>This determines the level where SVD considers values to be the |
| 3785 | | same. Default is 10<sup>-6</sup>. Make larger to where problems occur due to correlation. This is only available with the "Hessian" minimizers. |
| 3786 | | </DD><P></P> |
| 3787 | | <DT><B>Initial shift factor</B></DT> |
| 3788 | | <DD>A “damping multiplier” applied during the first refinement |
| 3789 | | cycle, for Jacobean/numeric refinements only. |
| 3790 | | Should be in interval (0.1, 100). See the |
| 3791 | | <A href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.optimize.leastsq.html">SciPy leastsq docs</A> |
| 3792 | | for more information. |
| 3793 | | </DD><P></P> |
| 3794 | | </DL> |
| 3795 | | <A name="SingleXtlSettings"></A> |
| 3796 | | <p style='margin-left:0.75in'><U>Single Crystal:</u><i> A set of controls is provided for |
| 3797 | | control of single-crystal refinements. |
| 3798 | | These only appear when single crystal (HKLF) histograms are present |
| 3799 | | in the project. </i> |
| 3800 | | </p> |
| 3801 | | <DL style='margin-left:1.0in'> |
| 3802 | | <DT><B>Refine HKLF as F^2?</B></DT> |
| 3803 | | <DD>When checked, refinements are against F<sup>2</sup> rather than |
| 3804 | | |F|. |
| 3805 | | </DD><P></P> |
| 3806 | | <DT><B>Min obs/sig</B></DT> |
| 3807 | | <DD>Conventional cutoff for single crystal refinements as to what reflections |
| 3808 | | should be considered observed, typical values are 2.0 (2σ) or 3.0 (3σ). |
| 3809 | | </DD><P></P> |
| 3810 | | <DT><B>Min extinct.</B></DT> |
| 3811 | | <DD>(needs further work) |
| 3812 | | </DD><P></P> |
| 3813 | | <DT><B>Max delt-F/sig</B></DT> |
| 3814 | | <DD>Removes reflections that are very poorly fit. Should be used |
| 3815 | | only with extreme care, since poorly-fit reflections could be an |
| 3816 | | indication that the structure is wrong. |
| 3817 | | </DD><P></P> |
| 3818 | | <DT><B>Max d-spacing</B></DT> |
| 3819 | | <DD>Reflections with d-space values larger than this value are ignored. |
| 3820 | | </DD><P></P> |
| 3821 | | <DT><B>Min d-spacing</B></DT> |
| 3822 | | <DD>Reflections with d-space values smaller than this value are ignored. |
| 3823 | | </DD><P></P> |
| 3824 | | |
| 3825 | | </DL> |
| 3826 | | |
| 3827 | | <A name="SequentialSettings"></A> |
| 3828 | | <p style='margin-left:0.75in'><U>Sequential Settings:</u><i> |
| 3829 | | A set of controls is for |
| 3830 | | sequential refinement. Settings here determine if a "normal" or "sequential" |
| 3831 | | refinement is performed. If no datasets are selected here, then all |
| 3832 | | histograms linked to phases in the project and that are flagged as |
| 3833 | | "used" are included in one potentially large (combined) |
| 3834 | | refinement. However, if any |
| 3835 | | number of histograms are selected here, then a |
| 3836 | | sequential refinement is performed, where a fit is made to the |
| 3837 | | structural model(s) fitting each selected |
| 3838 | | histogram in turn. Only the first item below is shown in "normal" mode. </i> |
| 3839 | | </p> |
| 3840 | | <DL style='margin-left:1.0in'> |
| 3841 | | <DT><B>Select datasets/Reselect Datasets</B></DT> |
| 3842 | | <DD>This brings up a menu where histograms can be selected, which |
| 3843 | | potentially switches between a normal and a sequential refinement. |
| 3844 | | If one or more histograms are selected, a sequential |
| 3845 | | refinement is used. If none are selected, then the refinement be |
| 3846 | | set as "normal". The button is labeled "Select" when in normal refinement |
| 3847 | | mode and "Reselect" in sequential refinement mode. |
| 3848 | | </DD><P></P> |
| 3849 | | <DT><B>Reverse order?</B></DT> |
| 3850 | | <DD>Normally, in a sequential histograms are fit in the order they |
| 3851 | | are in the data tree (which can be reordered by dragging tree |
| 3852 | | items), |
| 3853 | | but when this option is selected, the sequential fit is performed |
| 3854 | | with the last tree entry first. |
| 3855 | | </DD><P></P> |
| 3856 | | <DT><B>Copy results to next histogram?</B></DT> |
| 3857 | | <DD>When this option is selected, the fitted parameters from each |
| 3858 | | refinement are copied to the next histogram, so that the starting |
| 3859 | | point for each refinement will be the results from fitting the |
| 3860 | | previous. This works well for parametric experiments where |
| 3861 | | parameters such as the lattice parameters change gradually over |
| 3862 | | the course of successive measurements. |
| 3863 | | This option is usually used only for the initial refinement after |
| 3864 | | a sequential fit is started and the setting is reset once that |
| 3865 | | refinement is completed. For subsequent refinements, it is usually |
| 3866 | | better to start with the results from the previous fit. |
| 3867 | | </DD><P></P> |
| 3868 | | <DT><B>Clear previous seq. results</B></DT> |
| 3869 | | <DD>When this button is pressed, the "Sequential Results" entry |
| 3870 | | with the results from the last sequential fit is deleted from the |
| 3871 | | tree. |
| 3872 | | </DD><P></P> |
| 3873 | | </DL> |
| 3874 | | <p style='margin-left:0.75in'><U>Global Settings:</u><i> |
| 3875 | | This is a location for parameters that apply to an entire project. |
| 3876 | | At present there is only one. </i> |
| 3877 | | </p> |
| 3878 | | <DL style='margin-left:1.0in'> |
| 3879 | | <DT><B>CIF Author</B></DT> |
| 3880 | | <DD>The value provided here is used when creating a CIF of an |
| 3881 | | entire project. |
| 3882 | | </DD><P></P> |
| 3883 | | </DL> |
| 3884 | | |
| 3885 | | <h5 style='margin-left:.5in'><span |
| 3886 | | style='mso-fareast-font-family:"Times New Roman"'> |
| 3887 | | What can I do here?</span></h5> |
| 3888 | | <p style='margin-left:0.75in'>This offers a place to change how |
| 3889 | | GSAS-II performs refinements, but has no specific menu commands or |
| 3890 | | graphics. |
| 3891 | | </p> |
| 3892 | | |
| 3893 | | <h4 style='margin-left:0.25in'><a |
| 3894 | | name="Covariance">Covariance<a></h4> |
| 3895 | | |
| 3896 | | <p class=MsoNormal style='margin-left:.5in'> |
| 3897 | | This window contains final residual information; the GSASII |
| 3898 | | Plots window ‘Covariance’ shows a graphical |
| 3899 | | representation of the variance-covariance matrix. A text window is |
| 3900 | | displayed with statistical values and goodness of fit parameters. |
| 3901 | | </p> |
| 3902 | | |
| 3903 | | <h5 style='margin-left:.5in'> |
| 3904 | | What is plotted here?</h5> |
| 3905 | | <P style='margin-left:1.0in'> |
| 3906 | | The variance-covariance matrix as a color coded array is shown on this |
| 3907 | | page. The color bar to the right shows the range of covariances (-1 to |
| 3908 | | 1) and corresponding colors. The parameter names are to the right and |
| 3909 | | the parameter numbers are below the plot. |
| 3910 | | </P> |
| 3911 | | |
| 3912 | | <h5 style='margin-left:.5in'> |
| 3913 | | What can I do with the plot?</h5> |
| 3914 | | |
| 3915 | | <P style='margin-left:1.0in'> |
| 3916 | | Move the mouse cursor across the plot. If on a diagonal cell, the parameter name, |
| 3917 | | value and esd is shown both as a tool tip and in the right hand portion of the |
| 3918 | | status bar. If the cursor is off the diagonal, the two parameter names and |
| 3919 | | their covariance are shown in the tool tip and the status bar. |
| 3920 | | </P> |
| 3921 | | <P style='margin-left:1.0in'> |
| 3922 | | Use the Zoom and Pan buttons to focus on some |
| 3923 | | section of the variance-covariance matrix. |
| 3924 | | </p> |
| 3925 | | |
| 3926 | | <P style='margin-left:1.0in'> |
| 3927 | | Press |
| 3928 | | ‘s’ – A color scheme selection dialog is shown. Select a color scheme and press |
| 3929 | | OK, the new color scheme will be plotted. The default is ‘RdYlGn’. |
| 3930 | | </p> |
| 3931 | | <P style='margin-left:1.0in'> |
| 3932 | | Press ‘p’ – Saves the covariance values in a text file. |
| 3933 | | </p> |
| 3934 | | |
| 3935 | | <h4 style='margin-left:0.25in'><a name="Constraints"><span style='mso-fareast-font-family: |
| | 3816 | "Times New Roman"'>This window provides access to the controls that determine |
| | 3817 | how GSAS-II performs minimizations as well as few global parameters for |
| | 3818 | GSAS-II. Note that many other customization settings are set as <a |
| | 3819 | href="#Preferences">configuration variables</a> in the Preferences menu. (See |
| | 3820 | the <a |
| | 3821 | href="https://gsas-ii.readthedocs.io/en/latest/GSASIIutil.html#module-config_example">Programmer's |
| | 3822 | documentation</a> for a description of those.) <o:p></o:p></span></p> |
| | 3823 | |
| | 3824 | <p style='margin-left:.75in'><u>Refinement Controls:</u><i> These controls |
| | 3825 | determine how refinements are performed. The first determines the computational |
| | 3826 | engine used to minimize the structure. </i></p> |
| | 3827 | |
| | 3828 | <p class=MsoNormal style='margin-left:1.0in'><a name=RefineType></a><b><span |
| | 3829 | style='mso-fareast-font-family:"Times New Roman"'>Refinement type</span></b><span |
| | 3830 | style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p> |
| | 3831 | |
| | 3832 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3833 | "Times New Roman"'>This determines how refinements are performed. The choices |
| | 3834 | are:<o:p></o:p></span></p> |
| | 3835 | |
| | 3836 | <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto; |
| | 3837 | margin-left:1.25in;text-indent:-.25in;mso-list:l4 level1 lfo3;tab-stops:list .5in'><![if !supportLists]><span |
| | 3838 | style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol; |
| | 3839 | mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol'><span |
| | 3840 | style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'> |
| | 3841 | </span></span></span><![endif]><u><span style='mso-fareast-font-family:"Times New Roman"'>analytic |
| | 3842 | Hessian</span></u><span style='mso-fareast-font-family:"Times New Roman"'>: |
| | 3843 | This is the default option and is usually the most useful. It uses a |
| | 3844 | custom-developed least-squares minimizer that uses singular-value decomposition |
| | 3845 | (SVD) to reduce the errors caused by correlated variables and the |
| | 3846 | Levenberg-Marquardt algorithm to up-weight diagonal Hessian terms when |
| | 3847 | refinements fail to lower χ<sup>2</sup>. <o:p></o:p></span></p> |
| | 3848 | |
| | 3849 | <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto; |
| | 3850 | margin-left:1.25in;text-indent:-.25in;mso-list:l4 level1 lfo3;tab-stops:list .5in'><![if !supportLists]><span |
| | 3851 | style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol; |
| | 3852 | mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol'><span |
| | 3853 | style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'> |
| | 3854 | </span></span></span><![endif]><u><span style='mso-fareast-font-family:"Times New Roman"'>analytic |
| | 3855 | Jacobian</span></u><span style='mso-fareast-font-family:"Times New Roman"'>: |
| | 3856 | This uses a numpy-provided <i>leastsq</i> minimizer, which not applicable for problem |
| | 3857 | with a large number of histograms as it requires much more memory than the |
| | 3858 | Hessian routines. This because it creates a Jacobian matrix that is shaped N x |
| | 3859 | M (N parameters x M observations) while the Hessian methods create a Jacobian |
| | 3860 | matrix only each histogram. <o:p></o:p></span></p> |
| | 3861 | |
| | 3862 | <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto; |
| | 3863 | margin-left:1.25in;text-indent:-.25in;mso-list:l4 level1 lfo3;tab-stops:list .5in'><![if !supportLists]><span |
| | 3864 | style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol; |
| | 3865 | mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol'><span |
| | 3866 | style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'> |
| | 3867 | </span></span></span><![endif]><u><span style='mso-fareast-font-family:"Times New Roman"'>numeric</span></u><span |
| | 3868 | style='mso-fareast-font-family:"Times New Roman"'>: This also uses the numpy <i>leastsq</i> |
| | 3869 | minimizer, and is also not applicable for larger problems. Unlike, the |
| | 3870 | "analytic Jacobian", numerical derivatives are computed rather than |
| | 3871 | use the analytical derivatives that are coded directly into GSAS-II. This will |
| | 3872 | be slower than the analytical derivatives and will is often less accurate which |
| | 3873 | results in slower convergence. It is typically used for code development to |
| | 3874 | check the accuracy of the analytical derivative formulations. <o:p></o:p></span></p> |
| | 3875 | |
| | 3876 | <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto; |
| | 3877 | margin-left:1.25in;text-indent:-.25in;mso-list:l4 level1 lfo3;tab-stops:list .5in'><![if !supportLists]><span |
| | 3878 | style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol; |
| | 3879 | mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol'><span |
| | 3880 | style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'> |
| | 3881 | </span></span></span><![endif]><u><span style='mso-fareast-font-family:"Times New Roman"'>Hessian |
| | 3882 | SVD</span></u><span style='mso-fareast-font-family:"Times New Roman"'>: This is |
| | 3883 | very similar to <u>analytic Hessian</u> but does not include the |
| | 3884 | Levenberg-Marquardt algorithm. It can be faster, but is more prone to diverge |
| | 3885 | when severe correlation is present. It is possible that it might be better for |
| | 3886 | single-crystal refinements. <o:p></o:p></span></p> |
| | 3887 | |
| | 3888 | <p style='margin-left:1.25in'>Note that the Jacobian refinement tools are the |
| | 3889 | Fortran MINPACK <i>lmdif</i> and <i>lmder</i> algorithms wrapped in python as |
| | 3890 | provided in the Scipy package. The Hessian routines are were developed for |
| | 3891 | GSAS-II based on routines in numpy and scipy and using the material in |
| | 3892 | Numerical Recipes (Press, Flannery, Teulosky & Vetterling) for the |
| | 3893 | Levenberg-Marquardt. The purpose is to minimize the sum of the squares of M<span |
| | 3894 | style='mso-fareast-font-family:"Times New Roman"'> nonlinear functions in N |
| | 3895 | variables by a modification of the Levenberg-Marquardt algorithm. The lmdif and |
| | 3896 | lmder routines were written by </span>Burton S. Garbow, Kenneth E. Hillstrom, |
| | 3897 | Jorge J. More (Argonne National Laboratory, 1980). </p> |
| | 3898 | |
| | 3899 | <p class=MsoNormal style='margin-left:1.0in'><b><span style='mso-fareast-font-family: |
| | 3900 | "Times New Roman"'>Min delta-M/M</span></b><span style='mso-fareast-font-family: |
| | 3901 | "Times New Roman"'><o:p></o:p></span></p> |
| | 3902 | |
| | 3903 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3904 | "Times New Roman"'>A refinement will stop when the change in the minimization |
| | 3905 | function (M=Σ[w(Io-Ic)<sup>2</sup>]) is less than this value. The allowed range |
| | 3906 | is 10<sup>-9</sup> to 1.0, with a default of 0.001. A value of 1.0 stops the |
| | 3907 | refinement after a single cycle. Values less than 10<sup>-4</sup> cause |
| | 3908 | refinements to continue even if there is no meaningful improvement. <o:p></o:p></span></p> |
| | 3909 | |
| | 3910 | <p class=MsoNormal style='margin-left:1.0in'><b><span style='mso-fareast-font-family: |
| | 3911 | "Times New Roman"'>Max cycles</span></b><span style='mso-fareast-font-family: |
| | 3912 | "Times New Roman"'><o:p></o:p></span></p> |
| | 3913 | |
| | 3914 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3915 | "Times New Roman"'>This determines the maximum number of refinement cycles that |
| | 3916 | will be performed. This is only available with the "Hessian" |
| | 3917 | minimizers.<o:p></o:p></span></p> |
| | 3918 | |
| | 3919 | <p class=MsoNormal style='margin-left:1.0in'><b><span style='mso-fareast-font-family: |
| | 3920 | "Times New Roman"'>Initial lambda</span></b><span style='mso-fareast-font-family: |
| | 3921 | "Times New Roman"'><o:p></o:p></span></p> |
| | 3922 | |
| | 3923 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3924 | "Times New Roman"'>Note that here λ is the Marquardt coefficient, where a |
| | 3925 | weight of 1+λ is applied to the diagonal elements of the Hessian. When λ is |
| | 3926 | large, this down-weights the significance of the off-diagonal terms in the |
| | 3927 | Hessian. Thus, when λ is large, the refinement is effectively one of |
| | 3928 | steepest-descents, where correlation between variables is ignored. Note that |
| | 3929 | steepest-descents minimization is typically slow and may not always find the |
| | 3930 | local minimum. This is only available with the "analytical Hessian" |
| | 3931 | minimizer. <o:p></o:p></span></p> |
| | 3932 | |
| | 3933 | <p class=MsoNormal style='margin-left:1.0in'><b><span style='mso-fareast-font-family: |
| | 3934 | "Times New Roman"'>SVD zero tolerance</span></b><span style='mso-fareast-font-family: |
| | 3935 | "Times New Roman"'><o:p></o:p></span></p> |
| | 3936 | |
| | 3937 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3938 | "Times New Roman"'>This determines the level where SVD considers values to be |
| | 3939 | the same. Default is 10<sup>-6</sup>. Make larger to where problems occur due |
| | 3940 | to correlation. This is only available with the "Hessian" minimizers. |
| | 3941 | <o:p></o:p></span></p> |
| | 3942 | |
| | 3943 | <p class=MsoNormal style='margin-left:1.0in'><b><span style='mso-fareast-font-family: |
| | 3944 | "Times New Roman"'>Initial shift factor</span></b><span style='mso-fareast-font-family: |
| | 3945 | "Times New Roman"'><o:p></o:p></span></p> |
| | 3946 | |
| | 3947 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3948 | "Times New Roman"'>A “damping multiplier” applied during the first refinement |
| | 3949 | cycle, for Jacobean/numeric refinements only. Should be in interval (0.1, 100). |
| | 3950 | See the <a |
| | 3951 | href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.optimize.leastsq.html">SciPy |
| | 3952 | leastsq docs</a> for more information. <o:p></o:p></span></p> |
| | 3953 | |
| | 3954 | <p style='margin-left:.75in'><a name=SingleXtlSettings></a><u>Single Crystal:</u><i> |
| | 3955 | A set of controls is provided for control of single-crystal refinements. These |
| | 3956 | only appear when single crystal (HKLF) histograms are present in the project. </i></p> |
| | 3957 | |
| | 3958 | <p class=MsoNormal style='margin-left:1.0in'><b><span style='mso-fareast-font-family: |
| | 3959 | "Times New Roman"'>Refine HKLF as F^2?</span></b><span style='mso-fareast-font-family: |
| | 3960 | "Times New Roman"'><o:p></o:p></span></p> |
| | 3961 | |
| | 3962 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3963 | "Times New Roman"'>When checked, refinements are against F<sup>2</sup> rather |
| | 3964 | than |F|. <o:p></o:p></span></p> |
| | 3965 | |
| | 3966 | <p class=MsoNormal style='margin-left:1.0in'><b><span style='mso-fareast-font-family: |
| | 3967 | "Times New Roman"'>Min obs/sig</span></b><span style='mso-fareast-font-family: |
| | 3968 | "Times New Roman"'><o:p></o:p></span></p> |
| | 3969 | |
| | 3970 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3971 | "Times New Roman"'>Conventional cutoff for single crystal refinements as to |
| | 3972 | what reflections should be considered observed, typical values are 2.0 (2σ) or |
| | 3973 | 3.0 (3σ). <o:p></o:p></span></p> |
| | 3974 | |
| | 3975 | <p class=MsoNormal style='margin-left:1.0in'><b><span style='mso-fareast-font-family: |
| | 3976 | "Times New Roman"'>Min extinct.</span></b><span style='mso-fareast-font-family: |
| | 3977 | "Times New Roman"'><o:p></o:p></span></p> |
| | 3978 | |
| | 3979 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3980 | "Times New Roman"'>(needs further work) <o:p></o:p></span></p> |
| | 3981 | |
| | 3982 | <p class=MsoNormal style='margin-left:1.0in'><b><span style='mso-fareast-font-family: |
| | 3983 | "Times New Roman"'>Max delt-F/sig</span></b><span style='mso-fareast-font-family: |
| | 3984 | "Times New Roman"'><o:p></o:p></span></p> |
| | 3985 | |
| | 3986 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3987 | "Times New Roman"'>Removes reflections that are very poorly fit. Should be used |
| | 3988 | only with extreme care, since poorly-fit reflections could be an indication |
| | 3989 | that the structure is wrong. <o:p></o:p></span></p> |
| | 3990 | |
| | 3991 | <p class=MsoNormal style='margin-left:1.0in'><b><span style='mso-fareast-font-family: |
| | 3992 | "Times New Roman"'>Max d-spacing</span></b><span style='mso-fareast-font-family: |
| | 3993 | "Times New Roman"'><o:p></o:p></span></p> |
| | 3994 | |
| | 3995 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 3996 | "Times New Roman"'>Reflections with d-space values larger than this value are |
| | 3997 | ignored. <o:p></o:p></span></p> |
| | 3998 | |
| | 3999 | <p class=MsoNormal style='margin-left:1.0in'><b><span style='mso-fareast-font-family: |
| | 4000 | "Times New Roman"'>Min d-spacing</span></b><span style='mso-fareast-font-family: |
| | 4001 | "Times New Roman"'><o:p></o:p></span></p> |
| | 4002 | |
| | 4003 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 4004 | "Times New Roman"'>Reflections with d-space values smaller than this value are |
| | 4005 | ignored. <o:p></o:p></span></p> |
| | 4006 | |
| | 4007 | <p style='margin-left:.75in'><a name=SequentialSettings></a><u>Sequential |
| | 4008 | Settings:</u><i> A set of controls is for sequential refinement. Settings here |
| | 4009 | determine if a "normal" or "sequential" refinement is |
| | 4010 | performed. If no datasets are selected here, then all histograms linked to |
| | 4011 | phases in the project and that are flagged as "used" are included in |
| | 4012 | one potentially large (combined) refinement. However, if any number of |
| | 4013 | histograms are selected here, then a sequential refinement is performed, where |
| | 4014 | a fit is made to the structural model(s) fitting each selected histogram in |
| | 4015 | turn. Only the first item below is shown in "normal" mode. </i></p> |
| | 4016 | |
| | 4017 | <p class=MsoNormal style='margin-left:1.0in'><b><span style='mso-fareast-font-family: |
| | 4018 | "Times New Roman"'>Select datasets/Reselect Datasets</span></b><span |
| | 4019 | style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p> |
| | 4020 | |
| | 4021 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 4022 | "Times New Roman"'>This brings up a menu where histograms can be selected, |
| | 4023 | which potentially switches between a normal and a sequential refinement. If one |
| | 4024 | or more histograms are selected, a sequential refinement is used. If none are |
| | 4025 | selected, then the refinement be set as "normal". The button is |
| | 4026 | labeled "Select" when in normal refinement mode and |
| | 4027 | "Reselect" in sequential refinement mode. <o:p></o:p></span></p> |
| | 4028 | |
| | 4029 | <p class=MsoNormal style='margin-left:1.0in'><b><span style='mso-fareast-font-family: |
| | 4030 | "Times New Roman"'>Reverse order?</span></b><span style='mso-fareast-font-family: |
| | 4031 | "Times New Roman"'><o:p></o:p></span></p> |
| | 4032 | |
| | 4033 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 4034 | "Times New Roman"'>Normally, in a sequential histograms are fit in the order |
| | 4035 | they are in the data tree (which can be reordered by dragging tree items), but |
| | 4036 | when this option is selected, the sequential fit is performed with the last |
| | 4037 | tree entry first. <o:p></o:p></span></p> |
| | 4038 | |
| | 4039 | <p class=MsoNormal style='margin-left:1.0in'><b><span style='mso-fareast-font-family: |
| | 4040 | "Times New Roman"'>Copy results to next histogram?</span></b><span |
| | 4041 | style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p> |
| | 4042 | |
| | 4043 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 4044 | "Times New Roman"'>When this option is selected, the fitted parameters from |
| | 4045 | each refinement are copied to the next histogram, so that the starting point |
| | 4046 | for each refinement will be the results from fitting the previous. This works |
| | 4047 | well for parametric experiments where parameters such as the lattice parameters |
| | 4048 | change gradually over the course of successive measurements. This option is |
| | 4049 | usually used only for the initial refinement after a sequential fit is started |
| | 4050 | and the setting is reset once that refinement is completed. For subsequent |
| | 4051 | refinements, it is usually better to start with the results from the previous |
| | 4052 | fit. <o:p></o:p></span></p> |
| | 4053 | |
| | 4054 | <p class=MsoNormal style='margin-left:1.0in'><b><span style='mso-fareast-font-family: |
| | 4055 | "Times New Roman"'>Clear previous seq. results</span></b><span |
| | 4056 | style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p> |
| | 4057 | |
| | 4058 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 4059 | "Times New Roman"'>When this button is pressed, the "Sequential |
| | 4060 | Results" entry with the results from the last sequential fit is deleted |
| | 4061 | from the tree. <o:p></o:p></span></p> |
| | 4062 | |
| | 4063 | <p style='margin-left:.75in'><u>Global Settings:</u><i> This is a location for |
| | 4064 | parameters that apply to an entire project. At present there is only one. </i></p> |
| | 4065 | |
| | 4066 | <p class=MsoNormal style='margin-left:1.0in'><b><span style='mso-fareast-font-family: |
| | 4067 | "Times New Roman"'>CIF Author</span></b><span style='mso-fareast-font-family: |
| | 4068 | "Times New Roman"'><o:p></o:p></span></p> |
| | 4069 | |
| | 4070 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 4071 | "Times New Roman"'>The value provided here is used when creating a CIF of an |
| | 4072 | entire project. <o:p></o:p></span></p> |
| | 4073 | |
| | 4074 | <h5 style='margin-left:.5in'><span style='mso-fareast-font-family:"Times New Roman"'>What |
| | 4075 | can I do here?</span></h5> |
| | 4076 | |
| | 4077 | <p style='margin-left:.75in'>This offers a place to change how GSAS-II performs |
| | 4078 | refinements, but has no specific menu commands or graphics. </p> |
| | 4079 | |
| | 4080 | <h4 style='margin-left:.25in'><a name=Covariance>Covariance</a></h4> |
| | 4081 | |
| | 4082 | <p class=MsoNormal style='margin-left:.5in'>This window contains final residual |
| | 4083 | information; the GSASII Plots window ‘Covariance’ shows a graphical |
| | 4084 | representation of the variance-covariance matrix. A text window is displayed |
| | 4085 | with statistical values and goodness of fit parameters. </p> |
| | 4086 | |
| | 4087 | <h5 style='margin-left:.5in'>What is plotted here?</h5> |
| | 4088 | |
| | 4089 | <p style='margin-left:1.0in'>The variance-covariance matrix as a color coded |
| | 4090 | array is shown on this page. The color bar to the right shows the range of |
| | 4091 | covariances (-1 to 1) and corresponding colors. The parameter names are to the |
| | 4092 | right and the parameter numbers are below the plot. </p> |
| | 4093 | |
| | 4094 | <h5 style='margin-left:.5in'>What can I do with the plot?</h5> |
| | 4095 | |
| | 4096 | <p style='margin-left:1.0in'>Move the mouse cursor across the plot. If on a |
| | 4097 | diagonal cell, the parameter name, value and esd is shown both as a tool tip |
| | 4098 | and in the right hand portion of the status bar. If the cursor is off the |
| | 4099 | diagonal, the two parameter names and their covariance are shown in the tool |
| | 4100 | tip and the status bar. </p> |
| | 4101 | |
| | 4102 | <p style='margin-left:1.0in'>Use the Zoom and Pan buttons to focus on some |
| | 4103 | section of the variance-covariance matrix. </p> |
| | 4104 | |
| | 4105 | <p style='margin-left:1.0in'>Press ‘s’ – A color scheme selection dialog is |
| | 4106 | shown. Select a color scheme and press OK, the new color scheme will be |
| | 4107 | plotted. The default is ‘RdYlGn’. </p> |
| | 4108 | |
| | 4109 | <p style='margin-left:1.0in'>Press ‘p’ – Saves the covariance values in a text |
| | 4110 | file. </p> |
| | 4111 | |
| | 4112 | <h4 style='margin-left:.25in'><a name=Constraints><span style='mso-fareast-font-family: |
| 4370 | | <p style='margin-left:1.0in'>Menu <B>Commands</B> |
| 4371 | | </p> |
| 4372 | | |
| 4373 | | <p class=MsoListParagraphCxSpLast style='margin-left:1.5in;mso-add-space:auto; |
| 4374 | | text-indent:-.25in;mso-list:l27 level1 lfo15'> |
| 4375 | | a. <b>Error Analysis</b> |
| 4376 | | – this produces a ‘normal probability’ plot for the refinement result as |
| 4377 | | bounded by the limits. The slope and intercept of the curve in the central |
| 4378 | | region (-1 < / < 1) are shown on the |
| 4379 | | plot status line. The slope is the square root of GOF for the best fit set of |
| 4380 | | data points (~68% of the data).</p> |
| 4381 | | |
| 4382 | | <h5 style='margin-left:.5in'><span |
| 4383 | | style='mso-fareast-font-family:"Times New Roman"'> |
| 4384 | | What is plotted here?</span></h5> |
| 4385 | | <P style='margin-left:1.0in'> |
| 4386 | | The powder patterns that are |
| 4387 | | part of your project are shown on this page. They can be displayed as a stack |
| 4388 | | of powder patterns, just a single pattern or as a contour image of the peak |
| 4389 | | intensities. What can be done here will depend on home many patterns |
| 4390 | | are shown as well as what mode is selected. |
| 4391 | | Note that the tick marks and difference curve positions can be |
| 4392 | | customized, as <a href="#PWDR_dragticks">discussed below</a>. |
| 4393 | | </P><p class=MsoNormal style='margin-left:1.0in'> |
| 4394 | | Similar plots to the one here are displayed when different |
| 4395 | | subtree items are selected and on those plots it is possible to |
| 4396 | | view and in some cases edit information associated with the |
| 4397 | | histogram. As examples: |
| 4398 | | <UL style='margin-left:1.0in'> |
| 4399 | | <a name="otherPWDR"></a> |
| 4400 | | <LI>By selecting |
| 4401 | | the <a href="#PWDR_Limits">Limits</a> entry, range of data used, |
| 4402 | | as well as possible excluded regions, can be set. |
| 4403 | | <LI>Selecting <a href="#PWDR_Reflection_Lists">Reflection Lists</a> |
| 4404 | | allows display of reflection indicies (hkl values) for a |
| 4405 | | selected phase. |
| 4406 | | Letting the mouse rest unmoved at the position of a reflection |
| 4407 | | in 2-theta, Q, etc. (the vertical position does not matter) will |
| 4408 | | cause these to be displayed. After a short delay a |
| 4409 | | "tool tip" will appear with indicies for any reflections close |
| 4410 | | to the lateral mouse position. |
| 4411 | | <LI>Selecting <a href="#PWDR_Background">Background</a> allows |
| 4412 | | a mouse to be used to define |
| 4413 | | fixed points where a background curve |
| 4414 | | can be fitted to those points. |
| 4415 | | <LI>Selecting <a href="#PWDR_Instrument_Parameters">Instrument |
| 4416 | | Parameters</a>displays plot of peak widths as a function of 2theta |
| 4417 | | or Q. |
| 4418 | | <LI>Selecting <a href="#PWDR_Peak_List">Peak List</a> allows |
| 4419 | | postions of peaks to be defined for use in direct peak fitting. |
| 4420 | | <LI>Selecting <a href="#PWDR_Unit_Cells_List">Unit Cells List</a> |
| 4421 | | can show the positions of reflections for an arbitrary set of |
| 4422 | | unit cell parameters, optionally with space group extinctions |
| 4423 | | applied. |
| 4424 | | </P> |
| 4425 | | |
| 4426 | | </UL> |
| 4427 | | <h5 style='margin-left:.5in'><span |
| 4428 | | style='mso-fareast-font-family:"Times New Roman"'> |
| 4429 | | What can I do with the plot?</span></h5> |
| 4430 | | |
| 4431 | | <DL style='margin-left:0.5in'> |
| 4432 | | <DT>Move mouse |
| 4433 | | <DD>As the mouse cursor is moved across the plot, the plot status line |
| 4434 | | will show the cursor position as 2Theta, d-spacing and the |
| 4435 | | intensity. For a Q-plot, Q is shown instead of 2Theta. |
| 4436 | | |
| 4437 | | <DT>Press keyboard keys |
| 4438 | | <DD><a href="#PWDR_keylist">See below</a>. The "s" and "w" modes are commonly used. |
| 4439 | | |
| 4440 | | <a name="PWDR_dragticks"></a> |
| 4441 | | <DT>Drag tickmarks |
| 4442 | | <DD>Click on any tick mark and while holding the left mouse button |
| 4443 | | down move them to where you want them to |
| 4444 | | be displayed (press the s key for Sqrt(I) mode to reset to the |
| 4445 | | defaults). With multiple phases, clicking on the 2nd phase, |
| 4446 | | etc. changes the vertical spacing between phases. |
| 4447 | | Tick marks can be dragged only when the main PWDR or Reflection |
| 4448 | | Lists tree items are selected. |
| 4449 | | |
| 4450 | | <DT>Drag the difference curve |
| 4451 | | <DD>When the "normal" obs-calc plot is shown (as opposed to the |
| 4452 | | preferred "w" mode plot where (obs-calc)/sigma is displayed, click |
| 4453 | | on any point in the difference curve and while holding the left mouse button |
| 4454 | | down move the curve to where you want it to |
| 4455 | | be displayed (press the s key for Sqrt(I) mode to reset it to the |
| 4456 | | default). |
| 4457 | | The difference curve can be dragged only when the main PWDR or Reflection |
| 4458 | | Lists tree items are selected. |
| 4459 | | |
| 4460 | | <DT>Display/edit histogram information |
| 4461 | | <DD>By selecting different tree items within the current |
| 4462 | | histogram, it is possible to display and in some cases edit |
| 4463 | | information associated with the histogram. |
| 4464 | | <a href="#otherPWDR">See above.</a> |
| 4465 | | |
| 4466 | | <DT>Create a Publication-ready plot |
| 4467 | | <DD>Press the green "P" button to generate a customizable version |
| 4468 | | of the displayed plot that can be exported at high resolution. |
| 4469 | | </DL> |
| 4470 | | <a name="PWDR_keylist"></a><P style='margin-left:.5in'> |
| 4471 | | The following key press characters are defined (not for all plot |
| 4472 | | modes). These actions can also be initiated from the <B>Key Press</B> |
| 4473 | | button on the plot toolbar. </P> |
| 4474 | | <H4 style='margin-left:.5in'> |
| 4475 | | <I>For line plots:</I></H4> |
| 4476 | | <DL style='margin-left:0.75in'> |
| 4477 | | <DT><B> s: Sqrt(I) on/off</b><dd>changes the y-axis to be the |
| 4478 | | square-root of the intensity. The tick mark and the |
| 4479 | | difference curve location is reset. |
| 4480 | | <DT><B> w: toggle diff plot mode</b><dd>for the pattern selected from the |
| 4481 | | data tree, this will replace the difference (obs-calc) curve with |
| 4482 | | the differences divided by their standard uncertainty (esd) values |
| 4483 | | [(obs-calc)/sigma], which shows the significance of the deviations |
| 4484 | | in the fit of the pattern. <i>(Recommended)</I>. |
| 4485 | | <DT><B> b: subtract background</b><dd>Subtracts the fitted |
| 4486 | | background from the powder pattern. Pressing this again turns the |
| 4487 | | mode off. |
| 4488 | | <DT><B> n: log(I) on/off</b><dd>changes the y-axis to be the log10 of the intensity; difference |
| 4489 | | curve is not shown for log(I) on. |
| 4490 | | |
| 4491 | | <DT><B> q: toggle Q plot</b><dd>changes the x-axis from 2Theta to Q. |
| 4492 | | This will put multiple |
| 4493 | | powder patterns taken at different wavelengths/types on the same x-axis scale. |
| 4494 | | |
| 4495 | | <DT><B> t: toggle D-space plot</b><dd>changes the x-axis from 2Theta to d-space. |
| 4496 | | This will put multiple |
| 4497 | | powder patterns taken at different wavelengths/types on the same |
| 4498 | | x-axis scale. May not be very useful with data over a wide range. |
| 4499 | | |
| 4500 | | <DT><B> e: set excluded region</b> |
| 4501 | | <dd>Defines a new excluded region: press the "e" key with the mouse on |
| 4502 | | one side of the region. Move the mouse to the other side and and |
| 4503 | | press "e" again. The region markers (magenta dashed lines) can be |
| 4504 | | dragged to new positions. Available only when |
| 4505 | | the <a href="#PWDR_Limits">Limits</a> tree entry is selected. |
| 4506 | | <DT><B> x: show excluded region</b> |
| 4507 | | <dd>Normally all observed data is plotted. When the "x" key is |
| 4508 | | pressed, data inside excluded regions are not shown. |
| 4509 | | <DT><B> .: scaling diagnostic</b> |
| 4510 | | <dd>When the '.' key is pressed, data are plotted where the intensity |
| 4511 | | scale shows the equivalent number of counts so that uncertainty on |
| 4512 | | each point is the sqrt(I). |
| 4513 | | <DT><B> g: grid lines</b> |
| 4514 | | <dd>Draws vertical and horizontal grid lines at all axis label |
| 4515 | | positions. |
| 4516 | | <DT><B> a: add magnification region</b> |
| 4517 | | <dd>Adds a magnification region to the plot and sets the magnification |
| 4518 | | amount to x2. This can be edited (or deleted) in the table that is |
| 4519 | | shown when the main PWDR tree entry is selected. |
| 4520 | | |
| 4521 | | |
| 4522 | | </DL> |
| 4523 | | |
| 4524 | | <H4 style='margin-left:.5in'><I> |
| 4525 | | For line plots with more than one powder pattern: |
| 4526 | | </I></H4> |
| 4527 | | <DL style='margin-left:0.75in'> |
| 4528 | | <DT><B> c: contour on/off</b><dd>if multiple powder profiles, then a contour plot is shown |
| 4529 | | of the observed intensities. All data sets must be the same length as the first |
| 4530 | | one to be included in the contour plot. |
| 4531 | | <DT><B> S: set color Scheme</b> |
| 4532 | | <dd>Select the color map used for contour plots |
| 4533 | | |
| 4534 | | <DT><B> m: toggle single/multiple plot</b><dd>for multiple powder profiles, this will show only the one |
| 4535 | | selected from the data tree. The offset options (below) are not active. |
| 4536 | | <DT><B>f: select data</b><dd>Allows only some powder patterns to be |
| 4537 | | plotted, rather than all. |
| 4538 | | <DT><B> +,=: no selection</b><dd>for multiple powder profiles, only |
| 4539 | | the observed curve is shown when this mode is turned on ('+' and '=' |
| 4540 | | do exactly the same thing).</span></p> |
| 4541 | | <DT><B> /: normalize</b><dd>for multiple powder profiles, all |
| 4542 | | diffraction datasets are normalized so that the maximum intensity is 1. |
| 4543 | | </span></p> |
| 4544 | | </DL> |
| 4545 | | |
| 4546 | | <H4 style='margin-left:.5in'><I> |
| 4547 | | Offset modes for line plots in waterfall mode (multiple patterns only): |
| 4548 | | </I></H4> |
| 4549 | | <DL style='margin-left:0.75in'> |
| 4550 | | <DT><B>l: offset left</b><dd> |
| 4551 | | for a waterfall plot of multiple powder profiles, increase the |
| 4552 | | offset so that later plots are shifted more to the left relative to |
| 4553 | | previous plots. |
| 4554 | | |
| 4555 | | <DT><B>r: offset right</b><dd> |
| 4556 | | for a waterfall plot of multiple powder profiles, increase the |
| 4557 | | offset to the right (or decrease the left offset.) |
| 4558 | | |
| 4559 | | <DT><B> d,D: offset down</b><dd>for a waterfall plot of multiple |
| 4560 | | powder profiles, increase the offset down. |
| 4561 | | (D does the same as d but to a much larger amount) |
| 4562 | | |
| 4563 | | <DT><B> u,U: offset up</b><dd>for a waterfall plot of multiple powder |
| 4564 | | profiles, increase the offset up. |
| 4565 | | (U does the same as u but to a much larger amount) |
| 4566 | | |
| 4567 | | <DT><B> o: reset offset</b><dd>for a waterfall plot of multiple powder |
| 4568 | | profiles, reset to no offset. |
| 4569 | | </DL> |
| 4570 | | |
| 4571 | | <H4 style='margin-left:.5in'> |
| 4572 | | <I>For contour plots:</I></H4> |
| 4573 | | <DL style='margin-left:0.75in'> |
| 4574 | | <DT><B>d: lower contour max</b><DD> |
| 4575 | | this lowers the level chosen for the highest contour color. |
| 4576 | | <DT><B> |
| 4577 | | u: raise contour max</b><DD> |
| 4578 | | this raises the level chosen for the highest contour color |
| 4579 | | <DT><B> |
| 4580 | | i: interpolation method</b><DD> |
| 4581 | | this changes the method |
| 4582 | | used to represent the contours. If selected a dialog box appears with all the |
| 4583 | | possible choices. Default is ‘nearest’; the other useful choice is ‘bilinear’, |
| 4584 | | this will smooth out the contours. |
| 4585 | | <DT><B> |
| 4586 | | s: color scheme</b><DD> |
| 4587 | | this changes the color |
| 4588 | | scheme for the contouring. Default is ‘Paired’, black/ white options are |
| 4589 | | ‘Greys’ and ‘binary’ (for black on white) or ‘gray’ (for white on black). |
| 4590 | | Others can be very colorful (but not useful!) |
| 4591 | | <DT><B> |
| 4592 | | c: contour off/on</b><DD> |
| 4593 | | this turns off contouring |
| 4594 | | and returns to a waterfall plot with any offsets applied. |
| 4595 | | </DL> |
| 4596 | | |
| 4597 | | <H4 style='margin-left:.5in'><I> |
| 4598 | | For display of reflections from magnetic unit space groups |
| 4599 | | </I></H4> |
| 4600 | | <DL style='margin-left:0.75in'> |
| 4601 | | <DT><B>j: show next; reset use flag</b><dd> |
| 4602 | | Show the next magnetic space group in the list, clearing the "Use" |
| 4603 | | flag for the currently displayed space group. |
| 4604 | | (available from Index Unit Cells only). |
| 4605 | | <DT><B>k: show next</b><dd> |
| 4606 | | Show the next magnetic space group in the list. The "Use" |
| 4607 | | flag for the currently displayed space group is unchanged. |
| 4608 | | (available from Index Unit Cells only). |
| 4609 | | </DL> |
| 4610 | | <h4 style='margin-left:0.25in'><a name="PWDR_Comments"><u>Comments</u></a></h4> |
| 4611 | | |
| 4612 | | <p class=MsoNormal style='margin-left:.5in'>This |
| 4613 | | window shows whatever comment lines (preceded by “#”) found when the powder |
| 4614 | | data file was read by GSAS-II. If you are lucky, there will be useful |
| 4615 | | information here (e.g. sample name, date collected, wavelength used, etc.). If |
| 4616 | | not, this window will be blank. The text is read-only.</p> |
| 4617 | | |
| 4618 | | <h4 style='margin-left:0.25in'><a name="PWDR_Limits"><u> |
| 4619 | | Limits</u></a></h4> |
| 4620 | | |
| 4621 | | <p class=MsoNormal style='margin-left:.5in'> |
| 4622 | | This window shows the limits in position to be used in any |
| 4623 | | fitting for this powder pattern. The ‘original’ values are obtained from the |
| 4624 | | minimum & maximum values in the powder pattern. The ‘new’ values |
| 4625 | | determine the range of data that will be used in fitting. Units are |
| 4626 | | 2Theta for CW data and time (microsec) for TOF data. |
| 4627 | | </p> |
| | 4606 | <p style='margin-left:1.0in'>Menu <b>Commands</b> </p> |
| | 4607 | |
| | 4608 | <p class=MsoListParagraph style='margin-left:1.5in;mso-add-space:auto; |
| | 4609 | text-indent:-.25in;mso-list:l21 level1 lfo14'><![if !supportLists]><span |
| | 4610 | style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span |
| | 4611 | style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>a. <b>Error |
| | 4612 | Analysis</b> – this produces a ‘normal probability’ plot for the refinement |
| | 4613 | result as bounded by the limits. The slope and intercept of the curve in the |
| | 4614 | central region (-1 < / < 1) are shown on the plot status line. The slope |
| | 4615 | is the square root of GOF for the best fit set of data points (~68% of the |
| | 4616 | data).</p> |
| | 4617 | |
| | 4618 | <h5 style='margin-left:.5in'><span style='mso-fareast-font-family:"Times New Roman"'>What |
| | 4619 | is plotted here?</span></h5> |
| | 4620 | |
| | 4621 | <p style='margin-left:1.0in'>The powder patterns that are part of your project |
| | 4622 | are shown on this page. They can be displayed as a stack of powder patterns, |
| | 4623 | just a single pattern or as a contour image of the peak intensities. What can |
| | 4624 | be done here will depend on home many patterns are shown as well as what mode |
| | 4625 | is selected. Note that the tick marks and difference curve positions can be |
| | 4626 | customized, as <a href="#PWDR_dragticks">discussed below</a>. </p> |
| | 4627 | |
| | 4628 | <p class=MsoNormal style='margin-left:1.0in'>Similar plots to the one here are |
| | 4629 | displayed when different subtree items are selected and on those plots it is |
| | 4630 | possible to view and in some cases edit information associated with the |
| | 4631 | histogram. As examples: </p> |
| | 4632 | |
| | 4633 | <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto; |
| | 4634 | margin-left:1.0in;text-indent:-.25in;mso-list:l8 level1 lfo15;tab-stops:list .5in'><a |
| | 4635 | name=otherPWDR></a><![if !supportLists]><span style='font-size:10.0pt; |
| | 4636 | mso-bidi-font-size:12.0pt;font-family:Symbol;mso-fareast-font-family:Symbol; |
| | 4637 | mso-bidi-font-family:Symbol'><span style='mso-list:Ignore'>·<span |
| | 4638 | style='font:7.0pt "Times New Roman"'> |
| | 4639 | </span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>By |
| | 4640 | selecting the <a href="#PWDR_Limits">Limits</a> entry, range of data used, as |
| | 4641 | well as possible excluded regions, can be set. <o:p></o:p></span></p> |
| | 4642 | |
| | 4643 | <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto; |
| | 4644 | margin-left:1.0in;text-indent:-.25in;mso-list:l8 level1 lfo15;tab-stops:list .5in'><![if !supportLists]><span |
| | 4645 | style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol; |
| | 4646 | mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol'><span |
| | 4647 | style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'> |
| | 4648 | </span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>Selecting |
| | 4649 | <a href="#PWDR_Reflection_Lists">Reflection Lists</a> allows display of |
| | 4650 | reflection indicies (hkl values) for a selected phase. Letting the mouse rest |
| | 4651 | unmoved at the position of a reflection in 2-theta, Q, etc. (the vertical |
| | 4652 | position does not matter) will cause these to be displayed. After a short delay |
| | 4653 | a "tool tip" will appear with indicies for any reflections close to |
| | 4654 | the lateral mouse position. <o:p></o:p></span></p> |
| | 4655 | |
| | 4656 | <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto; |
| | 4657 | margin-left:1.0in;text-indent:-.25in;mso-list:l8 level1 lfo15;tab-stops:list .5in'><![if !supportLists]><span |
| | 4658 | style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol; |
| | 4659 | mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol'><span |
| | 4660 | style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'> |
| | 4661 | </span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>Selecting |
| | 4662 | <a href="#PWDR_Background">Background</a> allows a mouse to be used to define |
| | 4663 | fixed points where a background curve can be fitted to those points. <o:p></o:p></span></p> |
| | 4664 | |
| | 4665 | <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto; |
| | 4666 | margin-left:1.0in;text-indent:-.25in;mso-list:l8 level1 lfo15;tab-stops:list .5in'><![if !supportLists]><span |
| | 4667 | style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol; |
| | 4668 | mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol'><span |
| | 4669 | style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'> |
| | 4670 | </span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>Selecting |
| | 4671 | <a href="#PWDR_Instrument_Parameters">Instrument Parameters</a>displays plot of |
| | 4672 | peak widths as a function of 2theta or Q. <o:p></o:p></span></p> |
| | 4673 | |
| | 4674 | <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto; |
| | 4675 | margin-left:1.0in;text-indent:-.25in;mso-list:l8 level1 lfo15;tab-stops:list .5in'><![if !supportLists]><span |
| | 4676 | style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol; |
| | 4677 | mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol'><span |
| | 4678 | style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'> |
| | 4679 | </span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>Selecting |
| | 4680 | <a href="#PWDR_Peak_List">Peak List</a> allows postions of peaks to be defined |
| | 4681 | for use in direct peak fitting. <o:p></o:p></span></p> |
| | 4682 | |
| | 4683 | <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto; |
| | 4684 | margin-left:1.0in;text-indent:-.25in;mso-list:l8 level1 lfo15;tab-stops:list .5in'><![if !supportLists]><span |
| | 4685 | style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol; |
| | 4686 | mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol'><span |
| | 4687 | style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'> |
| | 4688 | </span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>Selecting |
| | 4689 | <a href="#PWDR_Unit_Cells_List">Unit Cells List</a> can show the positions of |
| | 4690 | reflections for an arbitrary set of unit cell parameters, optionally with space |
| | 4691 | group extinctions applied. <o:p></o:p></span></p> |
| | 4692 | |
| | 4693 | <h5 style='margin-left:.5in'><span style='mso-fareast-font-family:"Times New Roman"'>What |
| | 4694 | can I do with the plot?</span></h5> |
| | 4695 | |
| | 4696 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 4697 | "Times New Roman"'>Move mouse <o:p></o:p></span></p> |
| | 4698 | |
| | 4699 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 4700 | "Times New Roman"'>As the mouse cursor is moved across the plot, the plot |
| | 4701 | status line will show the cursor position as 2Theta, d-spacing and the |
| | 4702 | intensity. For a Q-plot, Q is shown instead of 2Theta. <o:p></o:p></span></p> |
| | 4703 | |
| | 4704 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 4705 | "Times New Roman"'>Press keyboard keys <o:p></o:p></span></p> |
| | 4706 | |
| | 4707 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 4708 | "Times New Roman"'><a href="#PWDR_keylist">See below</a>. The "s" and |
| | 4709 | "w" modes are commonly used. <a name="PWDR_dragticks"></a><o:p></o:p></span></p> |
| | 4710 | |
| | 4711 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 4712 | "Times New Roman"'>Drag tickmarks <o:p></o:p></span></p> |
| | 4713 | |
| | 4714 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 4715 | "Times New Roman"'>Click on any tick mark and while holding the left mouse |
| | 4716 | button down move them to where you want them to be displayed (press the s key |
| | 4717 | for Sqrt(I) mode to reset to the defaults). With multiple phases, clicking on |
| | 4718 | the 2nd phase, etc. changes the vertical spacing between phases. Tick marks can |
| | 4719 | be dragged only when the main PWDR or Reflection Lists tree items are selected. |
| | 4720 | <o:p></o:p></span></p> |
| | 4721 | |
| | 4722 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 4723 | "Times New Roman"'>Drag the difference curve <o:p></o:p></span></p> |
| | 4724 | |
| | 4725 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 4726 | "Times New Roman"'>When the "normal" obs-calc plot is shown (as |
| | 4727 | opposed to the preferred "w" mode plot where (obs-calc)/sigma is |
| | 4728 | displayed, click on any point in the difference curve and while holding the |
| | 4729 | left mouse button down move the curve to where you want it to be displayed |
| | 4730 | (press the s key for Sqrt(I) mode to reset it to the default). The difference |
| | 4731 | curve can be dragged only when the main PWDR or Reflection Lists tree items are |
| | 4732 | selected. <o:p></o:p></span></p> |
| | 4733 | |
| | 4734 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 4735 | "Times New Roman"'>Display/edit histogram information <o:p></o:p></span></p> |
| | 4736 | |
| | 4737 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 4738 | "Times New Roman"'>By selecting different tree items within the current |
| | 4739 | histogram, it is possible to display and in some cases edit information |
| | 4740 | associated with the histogram. <a href="#otherPWDR">See above.</a> <o:p></o:p></span></p> |
| | 4741 | |
| | 4742 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 4743 | "Times New Roman"'>Create a Publication-ready plot <o:p></o:p></span></p> |
| | 4744 | |
| | 4745 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 4746 | "Times New Roman"'>Press the green "P" button to generate a |
| | 4747 | customizable version of the displayed plot that can be exported at high |
| | 4748 | resolution. <o:p></o:p></span></p> |
| | 4749 | |
| | 4750 | <p style='margin-left:.5in'><a name="PWDR_keylist"></a>The following key press |
| | 4751 | characters are defined (not for all plot modes). These actions can also be |
| | 4752 | initiated from the <b>Key Press</b> button on the plot toolbar. </p> |
| | 4753 | |
| | 4754 | <h4 style='margin-left:.5in'>For line plots:</h4> |
| | 4755 | |
| | 4756 | <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family: |
| | 4757 | "Times New Roman"'>s: Sqrt(I) on/off</span></b><span style='mso-fareast-font-family: |
| | 4758 | "Times New Roman"'><o:p></o:p></span></p> |
| | 4759 | |
| | 4760 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 4761 | "Times New Roman"'>changes the y-axis to be the square-root of the intensity. |
| | 4762 | The tick mark and the difference curve location is reset. <o:p></o:p></span></p> |
| | 4763 | |
| | 4764 | <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family: |
| | 4765 | "Times New Roman"'>w: toggle diff plot mode</span></b><span style='mso-fareast-font-family: |
| | 4766 | "Times New Roman"'><o:p></o:p></span></p> |
| | 4767 | |
| | 4768 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 4769 | "Times New Roman"'>for the pattern selected from the data tree, this will |
| | 4770 | replace the difference (obs-calc) curve with the differences divided by their |
| | 4771 | standard uncertainty (esd) values [(obs-calc)/sigma], which shows the |
| | 4772 | significance of the deviations in the fit of the pattern. <i>(Recommended)</i>. |
| | 4773 | <o:p></o:p></span></p> |
| | 4774 | |
| | 4775 | <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family: |
| | 4776 | "Times New Roman"'>b: subtract background</span></b><span style='mso-fareast-font-family: |
| | 4777 | "Times New Roman"'><o:p></o:p></span></p> |
| | 4778 | |
| | 4779 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 4780 | "Times New Roman"'>Subtracts the fitted background from the powder pattern. |
| | 4781 | Pressing this again turns the mode off. <o:p></o:p></span></p> |
| | 4782 | |
| | 4783 | <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family: |
| | 4784 | "Times New Roman"'>n: log(I) on/off</span></b><span style='mso-fareast-font-family: |
| | 4785 | "Times New Roman"'><o:p></o:p></span></p> |
| | 4786 | |
| | 4787 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 4788 | "Times New Roman"'>changes the y-axis to be the log10 of the intensity; |
| | 4789 | difference curve is not shown for log(I) on. <o:p></o:p></span></p> |
| | 4790 | |
| | 4791 | <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family: |
| | 4792 | "Times New Roman"'>q: toggle Q plot</span></b><span style='mso-fareast-font-family: |
| | 4793 | "Times New Roman"'><o:p></o:p></span></p> |
| | 4794 | |
| | 4795 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 4796 | "Times New Roman"'>changes the x-axis from 2Theta to Q. This will put multiple |
| | 4797 | powder patterns taken at different wavelengths/types on the same x-axis scale. <o:p></o:p></span></p> |
| | 4798 | |
| | 4799 | <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family: |
| | 4800 | "Times New Roman"'>t: toggle D-space plot</span></b><span style='mso-fareast-font-family: |
| | 4801 | "Times New Roman"'><o:p></o:p></span></p> |
| | 4802 | |
| | 4803 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 4804 | "Times New Roman"'>changes the x-axis from 2Theta to d-space. This will put |
| | 4805 | multiple powder patterns taken at different wavelengths/types on the same |
| | 4806 | x-axis scale. May not be very useful with data over a wide range. <o:p></o:p></span></p> |
| | 4807 | |
| | 4808 | <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family: |
| | 4809 | "Times New Roman"'>e: set excluded region</span></b><span style='mso-fareast-font-family: |
| | 4810 | "Times New Roman"'> <o:p></o:p></span></p> |
| | 4811 | |
| | 4812 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 4813 | "Times New Roman"'>Defines a new excluded region: press the "e" key |
| | 4814 | with the mouse on one side of the region. Move the mouse to the other side and |
| | 4815 | and press "e" again. The region markers (magenta dashed lines) can be |
| | 4816 | dragged to new positions. Available only when the <a href="#PWDR_Limits">Limits</a> |
| | 4817 | tree entry is selected. <o:p></o:p></span></p> |
| | 4818 | |
| | 4819 | <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family: |
| | 4820 | "Times New Roman"'>x: show excluded region</span></b><span style='mso-fareast-font-family: |
| | 4821 | "Times New Roman"'> <o:p></o:p></span></p> |
| | 4822 | |
| | 4823 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 4824 | "Times New Roman"'>Normally all observed data is plotted. When the |
| | 4825 | "x" key is pressed, data inside excluded regions are not shown. <o:p></o:p></span></p> |
| | 4826 | |
| | 4827 | <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family: |
| | 4828 | "Times New Roman"'>.: scaling diagnostic</span></b><span style='mso-fareast-font-family: |
| | 4829 | "Times New Roman"'> <o:p></o:p></span></p> |
| | 4830 | |
| | 4831 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 4832 | "Times New Roman"'>When the '.' key is pressed, data are plotted where the |
| | 4833 | intensity scale shows the equivalent number of counts so that uncertainty on |
| | 4834 | each point is the sqrt(I). <o:p></o:p></span></p> |
| | 4835 | |
| | 4836 | <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family: |
| | 4837 | "Times New Roman"'>g: grid lines</span></b><span style='mso-fareast-font-family: |
| | 4838 | "Times New Roman"'> <o:p></o:p></span></p> |
| | 4839 | |
| | 4840 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 4841 | "Times New Roman"'>Draws vertical and horizontal grid lines at all axis label |
| | 4842 | positions. <o:p></o:p></span></p> |
| | 4843 | |
| | 4844 | <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family: |
| | 4845 | "Times New Roman"'>a: add magnification region</span></b><span |
| | 4846 | style='mso-fareast-font-family:"Times New Roman"'> <o:p></o:p></span></p> |
| | 4847 | |
| | 4848 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 4849 | "Times New Roman"'>Adds a magnification region to the plot and sets the |
| | 4850 | magnification amount to x2. This can be edited (or deleted) in the table that |
| | 4851 | is shown when the main PWDR tree entry is selected. <o:p></o:p></span></p> |
| | 4852 | |
| | 4853 | <h4 style='margin-left:.5in'>For line plots with more than one powder pattern: </h4> |
| | 4854 | |
| | 4855 | <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family: |
| | 4856 | "Times New Roman"'>c: contour on/off</span></b><span style='mso-fareast-font-family: |
| | 4857 | "Times New Roman"'><o:p></o:p></span></p> |
| | 4858 | |
| | 4859 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 4860 | "Times New Roman"'>if multiple powder profiles, then a contour plot is shown of |
| | 4861 | the observed intensities. All data sets must be the same length as the first |
| | 4862 | one to be included in the contour plot. <o:p></o:p></span></p> |
| | 4863 | |
| | 4864 | <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family: |
| | 4865 | "Times New Roman"'>S: set color Scheme</span></b><span style='mso-fareast-font-family: |
| | 4866 | "Times New Roman"'> <o:p></o:p></span></p> |
| | 4867 | |
| | 4868 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 4869 | "Times New Roman"'>Select the color map used for contour plots <o:p></o:p></span></p> |
| | 4870 | |
| | 4871 | <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family: |
| | 4872 | "Times New Roman"'>m: toggle single/multiple plot</span></b><span |
| | 4873 | style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p> |
| | 4874 | |
| | 4875 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 4876 | "Times New Roman"'>for multiple powder profiles, this will show only the one |
| | 4877 | selected from the data tree. The offset options (below) are not active. <o:p></o:p></span></p> |
| | 4878 | |
| | 4879 | <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family: |
| | 4880 | "Times New Roman"'>f: select data</span></b><span style='mso-fareast-font-family: |
| | 4881 | "Times New Roman"'><o:p></o:p></span></p> |
| | 4882 | |
| | 4883 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 4884 | "Times New Roman"'>Allows only some powder patterns to be plotted, rather than |
| | 4885 | all. <o:p></o:p></span></p> |
| | 4886 | |
| | 4887 | <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family: |
| | 4888 | "Times New Roman"'>+,=: no selection</span></b><span style='mso-fareast-font-family: |
| | 4889 | "Times New Roman"'><o:p></o:p></span></p> |
| | 4890 | |
| | 4891 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 4892 | "Times New Roman"'>for multiple powder profiles, only the observed curve is |
| | 4893 | shown when this mode is turned on ('+' and '=' do exactly the same thing).<o:p></o:p></span></p> |
| | 4894 | |
| | 4895 | <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family: |
| | 4896 | "Times New Roman"'>/: normalize</span></b><span style='mso-fareast-font-family: |
| | 4897 | "Times New Roman"'><o:p></o:p></span></p> |
| | 4898 | |
| | 4899 | <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: |
| | 4900 | "Times New Roman"'>for multiple powder profiles, all diffraction datasets are |
| | 4901 | normalized so that the maximum intensity is 1. <o:p></o:p></span></p> |
| | 4902 | |
| | 4903 | <h4 style='margin-left:.5in'>Offset modes for line plots in waterfall mode |
| | 4904 | (multiple patterns only): </h4> |
| | 4905 | |
| | 4906 | <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family: |
| | 4907 | "Times New Roman"'>l: offset left</span></b><span style='mso-fareast |
