Changeset 1930 for trunk/GSASIImath.py
 Timestamp:
 Jul 16, 2015 1:37:20 PM (8 years ago)
 File:

 1 edited
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trunk/GSASIImath.py
r1929 r1930 401 401 if j != Orig: 402 402 if AtNames[j] != notName: 403 Neigh.append([AtNames[j],dist[j] ])403 Neigh.append([AtNames[j],dist[j],True]) 404 404 Ids.append(Atoms[j][cia+8]) 405 405 return Neigh,[OId,Ids] 406 406 407 407 def AddHydrogens(AtLookUp,General,Atoms,AddHydId): 408 409 def getTransMat(RXYZ,OXYZ,TXYZ,Amat): 410 Vec = np.inner(Amat,np.array([OXYZTXYZ[0],RXYZTXYZ[0]])).T 411 Vec /= np.sqrt(np.sum(Vec**2,axis=1))[:,np.newaxis] 412 Mat2 = np.cross(Vec[0],Vec[1]) #UxV 413 Mat2 /= np.sqrt(np.sum(Mat2**2)) 414 Mat3 = np.cross(Mat2,Vec[0]) #(UxV)xU 415 return nl.inv(np.array([Vec[0],Mat2,Mat3])) 408 416 409 417 cx,ct,cs,cia = General['AtomPtrs'] … … 439 447 Ratom = GetAtomsById(Atoms,AtLookUp,[AddHydId[2],])[0] 440 448 RXYZ = np.array(Ratom[cx:cx+3]) 441 Vec = np.inner(Amat,np.array([OXYZTXYZ[0],RXYZTXYZ[0]])).T 442 Vec /= np.sqrt(np.sum(Vec**2,axis=1))[:,np.newaxis] 443 Mat2 = np.cross(Vec[0],Vec[1]) #UxV 444 Mat2 /= np.sqrt(np.sum(Mat2**2)) 445 Mat3 = np.cross(Mat2,Vec[0]) #(UxV)xU 446 iMat = nl.inv(np.array([Vec[0],Mat2,Mat3])) 449 iMat = getTransMat(RXYZ,OXYZ,TXYZ,Amat) 447 450 a = 0.96*cosd(70.5) 448 451 b = 0.96*sind(70.5) … … 460 463 Ratom = GetAtomsById(Atoms,AtLookUp,[AddHydId[2],])[0] 461 464 RXYZ = np.array(Ratom[cx:cx+3]) 462 Vec = np.inner(Amat,np.array([OXYZTXYZ[0],RXYZTXYZ[0]])).T 463 Vec /= np.sqrt(np.sum(Vec**2,axis=1))[:,np.newaxis] 464 Mat2 = np.cross(Vec[0],Vec[1]) #UxV 465 Mat2 /= np.sqrt(np.sum(Mat2**2)) 466 Mat3 = np.cross(Mat2,Vec[0]) #(UxV)xU 467 iMat = nl.inv(np.array([Vec[0],Mat2,Mat3])) 468 print 'add 2 H' 469 return [] 465 iMat = getTransMat(RXYZ,OXYZ,TXYZ,Amat) 466 a = 0.93*cosd(60.) 467 b = 0.93*sind(60.) 468 Hpos = [[a,b,0],[a,b,0]] 469 Hpos = np.inner(Bmat,np.inner(iMat,Hpos).T).T+OXYZ 470 return Hpos 470 471 else: #2 bonds 471 472 if 'C' in Oatom[ct]: … … 479 480 Ratom = GetAtomsById(Atoms,AtLookUp,[AddHydId[2],])[0] 480 481 RXYZ = np.array(Ratom[cx:cx+3]) 481 Vec = np.inner(Amat,np.array([OXYZTXYZ[0],RXYZTXYZ[0]])).T 482 Vec /= np.sqrt(np.sum(Vec**2,axis=1))[:,np.newaxis] 483 Mat2 = np.cross(Vec[0],Vec[1]) #UxV 484 Mat2 /= np.sqrt(np.sum(Mat2**2)) 485 Mat3 = np.cross(Mat2,Vec[0]) #(UxV)xU 486 iMat = nl.inv(np.array([Vec[0],Mat2,Mat3])) 482 iMat = getTransMat(RXYZ,OXYZ,TXYZ,Amat) 487 483 a = 0.82*cosd(70.5) 488 484 b = 0.82*sind(70.5)
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