fix minor bug of relax in abinit

Author: pipidog

DFTtoolbox/__pycache__/abinit.cpython-36.pyc

@@ -16,7 +16,7 @@ def ground(self,prefix,soc,mag,dftu,kdense=20):
         #spec=sorted(tuple(set(atom)))         
         atom, a_vec, sublat=self.getxsf(self.wkdir,prefix)
         klabel, kpath=self.getkpf(self.wkdir,prefix) 
-
+        
         # check if V<0, if yes, swap a1 and a2
         V=np.dot(np.cross(a_vec[0,:],a_vec[1,:]),a_vec[2,:])
         print('system volume={0} A^3'.format(V))
@@ -66,7 +66,6 @@ def ground(self,prefix,soc,mag,dftu,kdense=20):
         for n in range(0,len(atom)):
             file.write('  {0[0]:12.8f} {0[1]:12.8f} {0[2]:12.8f}  #  {1:>2s} ({2:>3d})\n'.\
                 format(sublat[n,:],ptable[atom[n]],(n+1)))
-            #file.write('%12.8f %12.8f %12.8f\n' % tuple(sublat[n,:].tolist()))
         file.write('\n')
         file.write('# Magnetism ======================================\n') 
         if mag=='on':
@@ -231,15 +230,17 @@ def relax(self,prefix):
         ptable=self.ptable()
         #spec=sorted(tuple(set(atom)))         
         atom, a_vec, sublat=self.getxsf(self.wkdir,prefix)
-        if type(atom[0])==str:
-            atom=[ self.__grep__(ptable,atn)[0] for atn in atom]     
+        
         # check if V<0, if yes, swap a1 and a2
         V=np.dot(np.cross(a_vec[0,:],a_vec[1,:]),a_vec[2,:])
         print('system volume={0} A^3'.format(V))
         if V < 0:
             print('Warning: V<0, a1/b1 and a2/b2 swapped, else abinit will report error!')
             a_vec=a_vec[[1,0,2],:]
-            sublat=sublat[:,[1,0,2]]    
+            sublat=sublat[:,[1,0,2]]   
+
+        if type(atom[0])==str:
+            atom=[ self.__grep__(ptable,atn)[0] for atn in atom]             
         # convert atomic name format to atomic number format
         spec=[]
         [spec.append(at_n) for at_n in atom if spec.count(at_n)==0]
@@ -275,7 +276,7 @@ def relax(self,prefix):
             file.write('  %12.8f %12.8f %12.8f\n' % tuple(a_vec[n,:].tolist()))       
         file.write('xred                    # atom in reduced coordinates\n')    
         for n in range(0,len(atom)):
-            file.write('  {0[0]:12.8f} {0[0]:12.8f} {0[0]:12.8f}  #  {1:>2s} ({2:>3d})\n'.\
+            file.write('  {0[0]:12.8f} {0[1]:12.8f} {0[2]:12.8f}  #  {1:>2s} ({2:>3d})\n'.\
                 format(sublat[n,:],ptable[atom[n]],(n+1)))
         file.write('\n')
         file.write('# Plane Waves ================================\n')

DFTtoolbox/__pycache__/qe.cpython-36.pyc

@@ -37,7 +37,7 @@ def ground(self,prefix,soc,mag,dftu,kdense=20):
         file.write('  max_seconds =  21000 ,\n')
         file.write('/\n')
         file.write('&SYSTEM\n')
-        file.write('  ! -- < basic parameters > --\n')
+        file.write('  ! < basic parameters > ===================\n')
         file.write('  ibrav = 0,\n')
         file.write('  celldm(1) = 1.89,\n')
         file.write('  ntyp = {0} ,\n'.format(len(spec)))
@@ -46,7 +46,7 @@ def ground(self,prefix,soc,mag,dftu,kdense=20):
         file.write('  ecutrho = 330 ,                     ! 4*ecutwfc for paw/ncpp, 10*ecutwfc for uspp\n')
         file.write('  occupations = \'smearing\' ,\n')
         file.write('  degauss = 0.02 ,\n')
-        file.write('  ! -- < spin wavefunctions > --\n')
+        file.write('  ! < spin wavefunctions > =================\n')
         if (soc is 'on'):
             file.write('  nspin = 4,\n')
             file.write('  noncolin = .true. ,\n')
@@ -57,18 +57,18 @@ def ground(self,prefix,soc,mag,dftu,kdense=20):
         elif (soc is 'off') and (mag is 'off'):
             file.write('  nspin = 1,\n')
         if (mag is 'on'):
-            file.write('  ! -- < magnetic constrains > --\n')
+            file.write('  ! < magnetic constrains > ================\n')
             file.write('  constrained_magnetization = \'none\'  ! constrain scheme\n')
             file.write('  lambda = 1.0                        ! constraint parameters, 0~1000\n')   
             file.write('  tot_magnetization=-1                ! major-s - minor-s (LSDA) > 0, if constrained_magnetization=\'total\'\n')
-            file.write('  ! -- < initial moments > --\n')
+            file.write('  ! < initial moments > ====================\n')
             for n in range(0,len(spec)):
                 file.write('  starting_magnetization({0}) = 0.0,    ! -1~+1, % of polar-valence-e\n'.format(n+1))
                 if (soc is 'on'):
                     file.write('  angle1({0}) = 0.0,                    ! angle between m and z\n'.format(n+1))
                     file.write('  angle2({0}) = 0.0,                    ! angle between m on x-y plane and x\n'.format(n+1))
         if (dftu is 'on'):
-            file.write('  ! -- < DFT+U parameters > --\n')
+            file.write('  ! < DFT+U parameters > ===================\n')
             file.write('  lda_plus_u = .true. \n')
             if (soc is 'off'):
                 file.write('  lda_plus_u_kind = 0\n')