mirror of https://github.com/QMCPACK/qmcpack.git
gamess analyzer, trimer structure
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6562 e5b18d87-469d-4833-9cc0-8cdfa06e9491
This commit is contained in:
Jaron Krogel
parent
dea5d759ca
commit
6fed27af80
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@ -105,7 +105,7 @@ class TextFile(DevBase):
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if pos!=-1:
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return self.mm.seek(pos,0)
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else:
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return None
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return -1
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#end if
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else:
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return self.mm.seek(pos,whence)
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@ -33,6 +33,26 @@ def assign_value(host,dest,file,string):
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class GamessAnalyzer(SimulationAnalyzer):
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lset_full = 'spdfg'
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lxyz = obj(
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s = set('s'.split()),
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p = set('x y z'.split()),
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d = set('xx yy zz xy xz yz'.split()),
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f = set('xxx yyy zzz xxy xxz yyx yyz zzx zzy xyz'.split()),
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g = set('xxxx yyyy zzzz xxxy xxxz yyyx yyyz zzzx zzzy xxyy xxzz yyzz xxyz yyxz zzxy'.split()),
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)
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lxyz_reverse = obj()
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for l,xyzs in lxyz.iteritems():
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for xyz in xyzs:
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lxyz_reverse[xyz] = l
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#end for
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#end for
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def __init__(self,arg0=None,prefix=None,analyze=False,exit=False,**outfilenames):
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self.info = obj(
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exit = exit,
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@ -111,27 +131,11 @@ class GamessAnalyzer(SimulationAnalyzer):
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def analyze_log(self):
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# read the log file
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log = self.get_output('output')
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# try to get the energy components
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energy = obj()
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try:
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if log!=None and log.seek('ENERGY COMPONENTS',0)!=-1:
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for n in xrange(18):
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line = log.readline()
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if '=' in line and 'ENERGY' in line:
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nameline,value = line.split('=')
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tokens = nameline.lower().split()
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name = ''
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for token in tokens:
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if token!='energy':
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name += token.replace('-','_')+'_'
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#end if
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#end for
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name = name[:-1]
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value = float(value.strip())
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energy[name]=value
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#end if
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#end for
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#end if
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self.read_energy_components(log,energy)
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except:
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if self.info.exit:
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self.error('log file analysis failed (energy components)')
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@ -140,23 +144,279 @@ class GamessAnalyzer(SimulationAnalyzer):
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if len(energy)>0:
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self.energy = energy
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#end if
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# try to get the orbital count from the log file
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counts = obj()
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try:
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if log.seek('TOTAL NUMBER OF MOS IN VARIATION SPACE',0)!=-1:
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if log.seek('TOTAL NUMBER OF BASIS SET SHELLS',0)!=-1:
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counts.shells = int(log.readtokens()[-1])
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#end if
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if log.seek('NUMBER OF CARTESIAN ATOMIC ORBITALS',0)!=-1:
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counts.cao = int(log.readtokens()[-1])
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#end if
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if log.seek('TOTAL NUMBER OF MOS IN VARIATION SPACE',1)!=-1:
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counts.mos = int(log.readtokens()[-1])
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#end if
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except:
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if self.info.exit:
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self.error('log file analysis failed (mo count)')
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self.error('log file analysis failed (counts)')
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#end if
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#end try
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if len(counts)>0:
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self.counts = counts
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#end if
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# try to get the up/down orbitals
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if 'counts' in self and False: # don't read orbitals, large
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orbitals = obj()
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try:
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self.read_orbitals(log,orbitals,'up' ,'-- ALPHA SET --')
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self.read_orbitals(log,orbitals,'down','-- BETA SET --' )
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except:
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if self.info.exit:
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self.error('log file analysis failed (orbitals)')
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#end if
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#end try
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if len(orbitals)>0:
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self.orbitals = orbitals
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#end if
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#end if
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# try to get the mulliken/lowdin populations in each ao
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if 'counts' in self:
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ao_populations = obj()
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self.read_ao_populations(log,ao_populations)
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try:
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self.read_ao_populations(log,ao_populations)
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except:
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if self.info.exit:
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self.error('log file analysis failed (ao populations)')
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#end if
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#end try
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if len(ao_populations)>0:
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self.ao_populations = ao_populations
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#end if
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#end if
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#end def analyze_log
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def read_energy_components(self,log,energy):
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if log!=None and log.seek('ENERGY COMPONENTS',0)!=-1:
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for n in xrange(18):
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line = log.readline()
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if '=' in line and 'ENERGY' in line:
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nameline,value = line.split('=')
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tokens = nameline.lower().split()
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name = ''
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for token in tokens:
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if token!='energy':
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name += token.replace('-','_')+'_'
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#end if
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#end for
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name = name[:-1]
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value = float(value.strip())
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energy[name]=value
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#end if
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#end for
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#end if
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#end def read_energy_components
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def read_orbitals(self,log,orbs,spec,header):
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success = True
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cao_tot = self.counts.cao
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mos_tot = self.counts.mos
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mos_found = 0
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eigenvalue = []
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symmetry = []
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coefficients = []
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have_basis = False
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element = []
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spec_index = []
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angular = []
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if log.seek(header,0)!=-1:
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imax = mos_tot
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jmax = 100
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i=0
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while mos_found<mos_tot and i<imax:
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j=0
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norbs = -1
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while j<jmax:
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line = log.readline()
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if line.strip().replace(' ','').isdigit():
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found_orbs = True
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norbs = len(line.split())
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break
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#end if
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j+=1
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#end while
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if j==jmax:
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success=False
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if self.info.exit:
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self.error('could not find start of orbitals for {0}\nnumber of orbitals read successfully: {1}\nnumber of orbitals not read: {2}'.format(header,mos_found,mos_tot-mos_found))
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else:
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break
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#end if
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#end if
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eigenvalue.extend(log.readtokens())
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symmetry.extend(log.readtokens())
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coeff = []
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for icao in xrange(cao_tot):
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tokens = log.readtokens()
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if not have_basis:
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e = tokens[1]
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element.append(e[0].upper()+e[1:].lower())
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spec_index.append(tokens[2])
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angular.append(tokens[3])
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#end if
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coeff.append(tokens[4:])
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#end for
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coefficients.extend(array(coeff,dtype=float).T)
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if not have_basis:
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stype = []
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ptype = []
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dtype = []
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ftype = []
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for ia in xrange(len(angular)):
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a = angular[ia].lower()
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if a in GamessAnalyzer.stypes:
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stype.append(ia)
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elif a in GamessAnalyzer.ptypes:
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ptype.append(ia)
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elif a in GamessAnalyzer.dtypes:
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dtype.append(ia)
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elif a in GamessAnalyzer.ftypes:
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ftype.append(ia)
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elif self.info.exit:
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self.error('unrecognized angular type: {0}'.format(angular[ia]))
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#end if
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#end for
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#end if
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have_basis = True
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mos_found = len(eigenvalue)
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i+=1
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#end while
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if i==imax:
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success=False
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if self.info.exit:
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self.error('orbital read failed for {0}\nnumber of orbitals read successfully: {1}\nnumber of orbitals not read: {2}'.format(header,mos_found,mos_tot-mos_found))
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#end if
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if success:
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orbs[spec] = obj(
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eigenvalue = array(eigenvalue ,dtype=float),
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symmetry = array(symmetry ,dtype=str ),
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coefficients = array(coefficients,dtype=float),
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basis = obj(
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element = array(element ,dtype=str),
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spec_index = array(spec_index,dtype=int),
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angular = array(angular ,dtype=str),
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stype = array(stype ,dtype=int),
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ptype = array(ptype ,dtype=int),
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dtype = array(dtype ,dtype=int),
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ftype = array(ftype ,dtype=int),
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)
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)
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#end if
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return success
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else:
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return False
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#end if
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#end def read_orbitals
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def read_ao_populations(self,log,ao_populations):
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cao_tot = self.counts.cao
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if log.seek('-- POPULATIONS IN EACH AO --',0)!=-1:
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log.readline()
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log.readline()
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mulliken = []
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lowdin = []
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element = []
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spec_index = []
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angular = []
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linds = obj()
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for l in GamessAnalyzer.lset_full:
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linds[l]=[]
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#end for
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for icao in xrange(cao_tot):
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tokens = log.readtokens()
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e = tokens[1]
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element.append(e[0].upper()+e[1:].lower())
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if len(tokens)==6:
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spec_index.append(tokens[2])
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angular.append(tokens[3])
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mulliken.append(tokens[4])
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lowdin.append(tokens[5])
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elif len(tokens)==5:
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spec_index.append(tokens[2][:-4])
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angular.append(tokens[2][-4:])
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mulliken.append(tokens[3])
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lowdin.append(tokens[4])
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#end if
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#end for
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for ia in xrange(len(angular)):
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a = angular[ia].lower()
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if a in GamessAnalyzer.lxyz_reverse:
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l = GamessAnalyzer.lxyz_reverse[a]
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linds[l].append(ia)
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elif self.info.exit:
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self.error('unrecognized angular type: {0}'.format(angular[ia]))
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#end if
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#end for
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mulliken = array(mulliken,dtype=float)
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lowdin = array(lowdin ,dtype=float)
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for l,lind in linds.iteritems():
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linds[l] = array(lind,dtype=int)
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#end for
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mulliken_shell = []
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lowdin_shell = []
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shell = obj()
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n=0
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for l in GamessAnalyzer.lset_full:
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if l in GamessAnalyzer.lxyz:
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lind = linds[l]
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nxyz = len(GamessAnalyzer.lxyz[l])
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nshell = len(lind)/nxyz
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shellinds = []
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for ns in range(nshell):
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inds = lind[ns*nxyz:(ns+1)*nxyz]
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mulliken_shell.append(mulliken[inds].sum())
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lowdin_shell.append(lowdin[inds].sum())
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shellinds.append(n)
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n+=1
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#end for
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shell[l] = array(shellinds,dtype=int)
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#end if
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#end for
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mulliken_shell = array(mulliken_shell)
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lowdin_shell = array(lowdin_shell)
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mulliken_angular = obj()
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lowdin_angular = obj()
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for l,shellinds in shell.iteritems():
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mulliken_angular[l] = mulliken_shell[shellinds].sum()
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lowdin_angular[l] = lowdin_shell[shellinds].sum()
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#end for
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basis = obj(
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element = array(element ,dtype=str),
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spec_index = array(spec_index,dtype=int),
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angular = array(angular ,dtype=str),
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)
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basis.transfer_from(linds)
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ao_populations.set(
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mulliken = mulliken,
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lowdin = lowdin,
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mulliken_shell = mulliken_shell,
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lowdin_shell = lowdin_shell,
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mulliken_angular = mulliken_angular,
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lowdin_angular = lowdin_angular,
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basis = basis,
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shell = shell,
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)
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#end if
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#end def read_ao_populations
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def analyze_punch(self):
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# read the punch file
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try:
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@ -141,7 +141,7 @@ class obj(AllAbilities):
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if header==None:
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header = self.__class__.__name__
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#end if
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self.log(header+post_header)
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self.log('\n'+header+post_header)
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self.log(pad+message.replace('\n','\n'+pad))
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if exit:
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self.log(' exiting.\n')
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@ -157,7 +157,7 @@ class obj(AllAbilities):
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if header==None:
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header=self.__class__.__name__
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#end if
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self.log(header+post_header)
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self.log('\n'+header+post_header)
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self.log(pad+message.replace('\n','\n'+pad))
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#end def warn
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@ -585,12 +585,12 @@ def generate_physical_system(**kwargs):
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#end if
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#end for
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type = kwargs['type']
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if type=='atom' or type=='dimer':
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if type=='atom' or type=='dimer' or type=='trimer':
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del kwargs['kshift']
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del kwargs['tiling']
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if not 'units' in kwargs:
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kwargs['units'] = 'B'
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#end if
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#if not 'units' in kwargs:
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# kwargs['units'] = 'B'
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##end if
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tiling = None
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else:
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tiling = kwargs['tiling']
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@ -2978,6 +2978,20 @@ class Structure(Sobj):
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lcur = 7
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#end if
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species = elem
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# relabel species that have multiple occurances
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sset = set(species)
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for spec in sset:
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if species.count(spec)>1:
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cnt=0
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for n in range(len(species)):
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specn = species[n]
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if specn==spec:
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cnt+=1
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species[n] = specn+str(cnt)
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#end if
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#end for
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#end if
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#end for
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elem = []
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for i in range(len(counts)):
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elem.extend(counts[i]*[species[i]])
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@ -4000,6 +4014,8 @@ def generate_structure(type='crystal',*args,**kwargs):
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s = generate_atom_structure(*args,**kwargs)
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elif type=='dimer':
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s = generate_dimer_structure(*args,**kwargs)
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elif type=='trimer':
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s = generate_trimer_structure(*args,**kwargs)
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elif type=='jellium':
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s = generate_jellium_structure(*args,**kwargs)
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elif type=='empty':
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@ -4007,7 +4023,7 @@ def generate_structure(type='crystal',*args,**kwargs):
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elif type=='basic':
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s = Structure(*args,**kwargs)
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else:
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Structure.class_error(str(type)+' is not a valid structure type\n options are crystal, defect, or atom')
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Structure.class_error(str(type)+' is not a valid structure type\n options are crystal, defect, atom, dimer, trimer, jellium, empty, or basic')
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#end if
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return s
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#end def generate_structure
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@ -4016,6 +4032,9 @@ def generate_structure(type='crystal',*args,**kwargs):
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def generate_atom_structure(atom=None,units='A',Lbox=None,skew=0,axes=None,kgrid=(1,1,1),kshift=(0,0,0),struct_type=Structure):
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if atom is None:
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Structure.class_error('atom must be provided','generate_atom_structure')
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#end if
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if Lbox!=None:
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axes = [[Lbox*(1-skew),0,0],[0,Lbox,0],[0,0,Lbox*(1+skew)]]
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#end if
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@ -4030,6 +4049,9 @@ def generate_atom_structure(atom=None,units='A',Lbox=None,skew=0,axes=None,kgrid
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def generate_dimer_structure(dimer=None,units='A',separation=None,Lbox=None,skew=0,axes=None,kgrid=(1,1,1),kshift=(0,0,0),struct_type=Structure,axis='x'):
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if dimer is None:
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Structure.class_error('dimer atoms must be provided to construct dimer','generate_dimer_structure')
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#end if
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if separation is None:
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Structure.class_error('separation must be provided to construct dimer','generate_dimer_structure')
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#end if
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@ -4055,6 +4077,69 @@ def generate_dimer_structure(dimer=None,units='A',separation=None,Lbox=None,skew
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#end def generate_dimer_structure
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def generate_trimer_structure(trimer=None,units='A',separation=None,angle=None,Lbox=None,skew=0,axes=None,kgrid=(1,1,1),kshift=(0,0,0),struct_type=Structure,axis='x',axis2='y',angular_units='degrees'):
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if trimer is None:
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Structure.class_error('trimer atoms must be provided to construct trimer','generate_trimer_structure')
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#end if
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if separation is None:
|
||||
Structure.class_error('separation must be provided to construct trimer','generate_trimer_structure')
|
||||
#end if
|
||||
if len(separation)!=2:
|
||||
Structure.class_error('two separation distances (atom1-atom2,atom1-atom3) must be provided to construct trimer\nyou provided {0} separation distances'.format(len(separation)),'generate_trimer_structure')
|
||||
#end if
|
||||
if angle is None:
|
||||
Structure.class_error('angle must be provided to construct trimer','generate_trimer_structure')
|
||||
#end if
|
||||
if angular_units=='degrees':
|
||||
angle *= pi/180
|
||||
elif not angle.startswith('rad'):
|
||||
Structure.class_error('angular units must be degrees or radians\nyou provided: {0}'.format(angle),'generate_trimer_structure')
|
||||
#end if
|
||||
if axis==axis2:
|
||||
Structure.class_error('axis and axis2 must be different to define the trimer plane\nyou provided {0} for both'.format(axis),'generate_trimer_structure')
|
||||
#end if
|
||||
if Lbox!=None:
|
||||
axes = [[Lbox*(1-skew),0,0],[0,Lbox,0],[0,0,Lbox*(1+skew)]]
|
||||
#end if
|
||||
p1 = [0,0,0]
|
||||
if axis=='x':
|
||||
p2 = [separation[0],0,0]
|
||||
elif axis=='y':
|
||||
p2 = [0,separation[0],0]
|
||||
elif axis=='z':
|
||||
p2 = [0,0,separation[0]]
|
||||
else:
|
||||
Structure.class_error('trimer bond1 (atom2-atom1) orientation axis must be x,y,z\n you provided: {0}'.format(axis),'generate_trimer_structure')
|
||||
#end if
|
||||
r = separation[1]
|
||||
c = cos(angle)
|
||||
s = sin(angle)
|
||||
axpair = axis+axis2
|
||||
if axpair=='xy':
|
||||
p3 = [r*c,r*s,0]
|
||||
elif axpair=='yx':
|
||||
p3 = [r*s,r*c,0]
|
||||
elif axpair=='yz':
|
||||
p3 = [0,r*c,r*s]
|
||||
elif axpair=='zy':
|
||||
p3 = [0,r*s,r*c]
|
||||
elif axpair=='zx':
|
||||
p3 = [r*s,0,r*c]
|
||||
elif axpair=='xz':
|
||||
p3 = [r*c,0,r*s]
|
||||
else:
|
||||
Structure.class_error('trimer bond2 (atom3-atom1) orientation axis must be x,y,z\n you provided: {0}'.format(axis2),'generate_trimer_structure')
|
||||
#end if
|
||||
if axes is None:
|
||||
s = Structure(elem=trimer,pos=[p1,p2,p3],units=units)
|
||||
else:
|
||||
s = Structure(elem=trimer,pos=[p1,p2,p3],axes=axes,kgrid=kgrid,kshift=kshift,units=units)
|
||||
s.center_molecule()
|
||||
#end if
|
||||
return s
|
||||
#end def generate_trimer_structure
|
||||
|
||||
|
||||
def generate_jellium_structure(*args,**kwargs):
|
||||
return Jellium(*args,**kwargs)
|
||||
#end def generate_jellium_structure
|
||||
|
|
|
|||
|
|
@ -40,10 +40,11 @@
|
|||
import os
|
||||
from numpy import array,abs,empty,ndarray
|
||||
from generic import obj
|
||||
from periodic_table import is_element
|
||||
from simulation import SimulationInput
|
||||
from structure import interpolate_structures,Structure
|
||||
from physical_system import PhysicalSystem
|
||||
from developer import DevBase
|
||||
from developer import DevBase,error
|
||||
from debug import *
|
||||
lcs = ls
|
||||
|
||||
|
|
@ -1008,7 +1009,11 @@ class Poscar(VFormattedFile):
|
|||
#end for
|
||||
if self.elem!=None:
|
||||
for e in self.elem:
|
||||
text += e+' '
|
||||
iselem,symbol = is_element(e,symbol=True)
|
||||
if not iselem:
|
||||
self.error('{0} is not an element'.format(e))
|
||||
#end if
|
||||
text += symbol+' '
|
||||
#end for
|
||||
text += '\n'
|
||||
#end if
|
||||
|
|
@ -1276,7 +1281,7 @@ class VaspInput(SimulationInput,Vobj):
|
|||
#end def write
|
||||
|
||||
|
||||
def incorporate_system(self,system,incorp_kpoints=True):
|
||||
def incorporate_system(self,system,incorp_kpoints=True,coord='cartesian'):
|
||||
structure = system.structure
|
||||
|
||||
# assign kpoints
|
||||
|
|
@ -1300,8 +1305,15 @@ class VaspInput(SimulationInput,Vobj):
|
|||
poscar.axes = s.axes
|
||||
poscar.elem = species
|
||||
poscar.elem_count = species_count
|
||||
poscar.coord = 'cartesian'
|
||||
poscar.pos = s.pos
|
||||
if coord=='cartesian':
|
||||
poscar.coord = 'cartesian'
|
||||
poscar.pos = s.pos
|
||||
elif coord=='direct':
|
||||
poscar.coord = 'direct'
|
||||
poscar.pos = s.pos_unit()
|
||||
else:
|
||||
self.error('coord must be either direct or cartesian\nyou provided: {0}'.format(coord))
|
||||
#end if
|
||||
if s.frozen!=None:
|
||||
poscar.dynamic = s.frozen==False
|
||||
#end if
|
||||
|
|
@ -1327,10 +1339,13 @@ class VaspInput(SimulationInput,Vobj):
|
|||
#end for
|
||||
ordered_pseudos = []
|
||||
for element in species:
|
||||
if not element in pseudo_map:
|
||||
self.error('pseudopotential for element {0} not found\nelements present: {1}\n'.format(element,sorted(pseudo_map.keys())))
|
||||
iselem,symbol = is_element(element,symbol=True)
|
||||
if not iselem:
|
||||
self.error('{0} is not an element'.format(element))
|
||||
elif not symbol in pseudo_map:
|
||||
self.error('pseudopotential for element {0} not found\nelements present: {1}'.format(symbol,sorted(pseudo_map.keys())))
|
||||
#end if
|
||||
ordered_pseudos.append(pseudo_map[element])
|
||||
ordered_pseudos.append(pseudo_map[symbol])
|
||||
#end for
|
||||
#end if
|
||||
self.potcar = Potcar(VaspInput.pseudo_dir,ordered_pseudos)
|
||||
|
|
@ -1453,7 +1468,8 @@ generate_any_defaults = obj(
|
|||
system = None,
|
||||
pseudos = None,
|
||||
neb = None,
|
||||
neb_args = obj()
|
||||
neb_args = obj(),
|
||||
coord = 'cartesian'
|
||||
)
|
||||
|
||||
def generate_any_vasp_input(**kwargs):
|
||||
|
|
@ -1500,7 +1516,7 @@ def generate_any_vasp_input(**kwargs):
|
|||
# incorporate system information
|
||||
species = None
|
||||
if vf.system!=None:
|
||||
species = vi.incorporate_system(vf.system,gen_kpoints)
|
||||
species = vi.incorporate_system(vf.system,gen_kpoints,vf.coord)
|
||||
#end if
|
||||
|
||||
# set potcar
|
||||
|
|
@ -1557,7 +1573,7 @@ def generate_any_vasp_input(**kwargs):
|
|||
|
||||
|
||||
|
||||
def generate_poscar(structure):
|
||||
def generate_poscar(structure,coord='cartesian'):
|
||||
s = structure.copy()
|
||||
s.change_units('A')
|
||||
species,species_count = s.order_by_species()
|
||||
|
|
@ -1566,8 +1582,15 @@ def generate_poscar(structure):
|
|||
poscar.axes = s.axes
|
||||
poscar.elem = species
|
||||
poscar.elem_count = species_count
|
||||
poscar.coord = 'cartesian'
|
||||
poscar.pos = s.pos
|
||||
if coord=='cartesian':
|
||||
poscar.coord = 'cartesian'
|
||||
poscar.pos = s.pos
|
||||
elif coord=='direct':
|
||||
poscar.coord = 'direct'
|
||||
poscar.pos = s.pos_unit()
|
||||
else:
|
||||
error('coord must be either direct or cartesian\nyou provided: {0}'.format(coord),'generate_poscar')
|
||||
#end if
|
||||
if s.frozen!=None:
|
||||
poscar.dynamic = s.frozen==False
|
||||
#end if
|
||||
|
|
|
|||
Loading…
Reference in New Issue