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Commit b7cccee8 authored by Ask Hjorth Larsen's avatar Ask Hjorth Larsen
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all molcas modules now either parsed or explicitly ignored. Typically parse... 

all molcas modules now either parsed or explicitly ignored.  Typically parse the kind of method and the total energy.  Relentlessly hacked SMs until the damn thing worked.
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parser/parser-molcas/main.py
+ 165
− 35
View file @ b7cccee8
......@@ -113,8 +113,14 @@ class MolcasContext(object):
# XXX distinguish somehow between these two?
esm = 'DFT'
xc = ['HF_X']
elif method in ['RASSCF', 'RAS-CI', 'CASPT2']:
elif method in ['RASSCF', 'RAS-CI', 'CASPT2', 'CCSDT']:
esm = method
elif method in ['CASVB', 'MRCI']:
esm = 'MRCISD'
elif method == 'MCPF':
esm = method ## Not defined by nomad
elif method == 'MBPT2':
esm = 'MP2'
elif method in functionals:
esm = 'DFT'
xc = functionals[method]
......@@ -216,12 +222,12 @@ class MolcasContext(object):
context = MolcasContext()
def get_inputfile_echo_sm():
m = SM(r'\+\+\s*----+\s*Input file\s*---+',
endReStr='--\s*-------+',
sections=['section_method'],
name='inputfile')
return m
#def get_inputfile_echo_sm():
# m = SM(r'\+\+\s*----+\s*Input file\s*---+',
# endReStr='--\s*-------+',
# sections=['section_method'],
# name='inputfile')
# return m
def get_system_sm():
......@@ -247,7 +253,7 @@ def get_finalresults_sm(): # Other modes than SCF/KS-DFT?
sections=['section_single_configuration_calculation'],
name='results',
subMatchers=[
SM(r'\s*Total SCF energy\s*(?P<energy_total__eV>\S+)', name='etot') # XXX eV?
SM(r'\s*Total SCF energy\s*(?P<energy_total__hartree>\S+)', name='etot')
])
return m
......@@ -267,12 +273,36 @@ molcas_modules = ('alaska|caspt2|casvb|ccsdt|cpf|expbas|ffpt|gateway|'
'mckinley|mclr|motra|mrci|numerical_gradient|rasscf|'
'rassi|scf|seward|slapaf|vibrot').split('|')
ignore_modules = {'alaska', # OK
'numerical_gradient', # OK
'rassi', # OK
'motra',
'guga',
'ffpt',
'genano',
'grid_it',
'loprop',
'guessorb',
'expbas',
'vibrot',
'mckinley'
#'last_energy',
}
def get_anymodule_sms():
sms = []
for modulename in molcas_modules:
sms.append(SM(r'--- Start Module:\s*%s' % modulename, name=modulename))
#sms.append(SM(r'\s*MOLCAS executing module %s' % modulename.upper(),
# name=modulename))
adhoc = None
if modulename not in ignore_modules:
class AdHoc:
def __init__(self, name):
self.name = name
def __call__(self, parser):
raise ValueError('module: %s' % self.name)
adhoc = AdHoc(modulename)
sms.append(SM(r'--- Start Module:\s*%s' % modulename,
adHoc=adhoc,
name=modulename))
return sms
#def module_sm(name, *args, **kwargs):
......@@ -295,6 +325,57 @@ def mw(modname, *args, **kwargs):
])
return m
def mod_pattern(lower, upper=None):
if upper is None:
upper = lower.upper()
return (r'---\s*Start Module:\s*{0}|'
r'\s*MOLCAS executing module\s*{1}'.format(lower, upper))
# Define these separately or not?
def startmod_pattern(name):
return r'---\s*Start Module:\s*{}'.format(name)
def execmod_pattern(name):
return r'\s*MOLCAS executing module\s*{}'.format(name)
def gateway_seward():
m = SM(mod_pattern(r'(:?gateway|seward)'),
#weak=True,
name='gate/seward',
#r'\s*MOLCAS executing module (GATEWAY|SEWARD)', name='seward',
subMatchers=[
get_system_sm()
])
return m
def scf_rasscf():
m = SM(mod_pattern(r'(:?ras)?scf'),
name='(ras)scf', #r'(?:ras)?scf', r'\s*MOLCAS executing module (?:SCF|RASSCF)', name='scf',
#sections=['section_method', 'section_single_configuration_calculation'],
subMatchers=[ # XXX opens method section even if there is no outpout
SM(r'\s*(?P<x_molcas_method_name>.*?)\s*iterations: Energy and convergence statistics',
sections=['section_method'],
name='scfiter'),
SM(r'\s*CI only, no orbital optimization',
sections=['section_method'],
fixedStartValues={'x_molcas_method_name': 'RAS-CI'}),
SM(r'\s*Total SCF energy\s*(?P<energy_total__hartree>\S+)', name='E-tot',
sections=['section_single_configuration_calculation']),
SM(r'\s*RASSCF root number\s*\d+\s*Total energy\s*=\s*(?P<energy_total__hartree>\S+)', name='E-ras',
sections=['section_single_configuration_calculation']),
])
return m
def caspt2():
m = SM(mod_pattern(r'caspt2'),
#caspt2', r'\s*MOLCAS executing module CASPT2',
name='caspt2', # XXX opens section even if there is no output
sections=['section_method', 'section_single_configuration_calculation'],
fixedStartValues={'x_molcas_method_name': 'CASPT2'},
subMatchers=[
SM(r'\s*Total energy:\s*(?P<energy_total__hartree>\S+)', name='E-caspt2')
])
return m
def molcas_main_loop_sm():
m = SM(r'--- Start Module:\s*(?:%s)' % '|'.join(molcas_modules),
endReStr='--- Stop Module:',
......@@ -302,29 +383,12 @@ def molcas_main_loop_sm():
forwardMatch=True,
name='module',
subMatchers=[
mw(r'(gateway|seward)',
r'\s*MOLCAS executing module (GATEWAY|SEWARD)', name='seward',
subMatchers=[
get_system_sm()
]),
mw(r'(?:ras)?scf', r'\s*MOLCAS executing module (?:SCF|RASSCF)', name='scf',
sections=['section_method', 'section_single_configuration_calculation'],
subMatchers=[
SM(r'\s*(?P<x_molcas_method_name>.*?)\s*iterations: Energy and convergence statistics',
name='scfiter'),
SM(r'\s*CI only, no orbital optimization',
fixedStartValues={'x_molcas_method_name': 'RAS-CI'}),
SM(r'\s*Total SCF energy\s*(?P<energy_total__hartree>\S+)', name='E-tot'),
SM(r'\s*RASSCF root number\s*\d+\s*Total energy\s*=\s*(?P<energy_total__hartree>\S+)', name='E-ras'),
]),
mw(r'caspt2', r'\s*MOLCAS executing module CASPT2',
name='caspt2',
sections=['section_method', 'section_single_configuration_calculation'],
fixedStartValues={'x_molcas_method_name': 'CASPT2'},
subMatchers=[
SM(r'\s*Total energy:\s*(?P<energy_total__hartree>\S+)', name='E-caspt2')
]),
mw(r'slapaf', r'\s*MOLCAS executing module (SLAPAF)|\s*Specification of the internal coordinates according to the user-defined',
gateway_seward(),
scf_rasscf(),
caspt2(),
SM(r'%s|%s' % (mod_pattern(r'slapaf'),
# Sometimes the damn thing starts without a proper header!! ARGH!
r's*Specification of the internal coordinates according to the user-defined'),
name='slapaf',
subMatchers=[
SM(r'\*\s*Energy Statistics for Geometry Optimization',
......@@ -345,7 +409,73 @@ def molcas_main_loop_sm():
r'\s*ATOM\s*X\s*Y\s*Z',
r'\s*(\S+)\s*(\S+)\s*(\S+)\s*(\S+)')
])
])
]),
# last_energy just means it calls some other modules with annoyingly irregular output format
SM(mod_pattern(r'last_energy'),
name='last',
subMatchers=[
gateway_seward(),
scf_rasscf(),
caspt2(),
]),
SM(mod_pattern('casvb'),
name='casvb',
sections=['section_method'],
fixedStartValues={'x_molcas_method_name': 'CASVB'},
subMatchers=[
SM('\s*CASSCF energy\s*:\s*(?P<energy_total__hartree>\S+)',
sections=['section_single_configuration_calculation'],
name='e-tot')
]),
SM(mod_pattern('mrci'),
name='mrci',
sections=['section_method'],
fixedStartValues={'x_molcas_method_name': 'MRCI'},
subMatchers=[
SM(r'\s*CI ENERGY:\s*(?P<energy_total__hartree>\S+)',
sections=['section_single_configuration_calculation'])
]),
SM(mod_pattern('cpf', 'CPFMCPF'),
name='cpf',
sections=['section_method'],
fixedStartValues={'x_molcas_method_name': 'MCPF'},
subMatchers=[
SM(r'\s*FINAL MCPF ENERGY\s*(?P<energy_total__hartree>\S+)',
sections=['section_single_configuration_calculation'])
]),
SM(mod_pattern('ccsdt', r'CCSD\(T\)'),
name='ccsdt',
sections=['section_method'],
fixedStartValues={'x_molcas_method_name': 'CCSDT'},
subMatchers=[
SM(r'\s*Total energy \(diff\)\s*:\s*(?P<energy_total__hartree>\S+)',
sections=['section_single_configuration_calculation'])
]),
SM(mod_pattern('mbpt2'),
name='mbpt2',
fixedStartValues={'x_molcas_method_name': 'MBPT2'},
sections=['section_method', 'section_single_configuration_calculation'],
subMatchers=[
SM(r'\s*Total energy\s*=\s*(?P<energy_total__hartree>\S+)\s*a\.u\.')
]),
SM(mod_pattern('mclr'),
name='mclr',
subMatchers=[
SM(r'\s*\*\s*Harmonic frequencies in cm-1\s*\*',
endReStr=r'\s*\*\s*THERMOCHEMISTRY',
sections=['section_single_configuration_calculation'],
subMatchers=[
SM(r'\s*Symmetry\s*(?P<x_molcas_frequency_symmetry>\S+)',
name='symm',
repeats=True,
sections=['x_molcas_section_frequency'],
subMatchers=[
SM(r'\s*Freq\.\s*i(?P<x_molcas_imaginary_frequency_value__cm_1>\S+)', name='ifreq'),
SM(r'\s*Freq\.\s*(?P<x_molcas_frequency_value>\S+)', name='freq'),
SM(r'\s*Intensity:\s*(?P<x_molcas_frequency_intensity__km_mol_1>\S+)', name='intensity')
])
]),
]),
] + get_anymodule_sms())
return m
......
parser/parser-molcas/runtests.py
+ 3
− 1
View file @ b7cccee8
......@@ -38,12 +38,14 @@ for i, testfile in enumerate(testfiles):
if i % world.size != world.rank:
continue
dirname, basename = os.path.split(testfile)
print(basename)
#print(testfile)
#print(basename)
py = 'python'
if platform.node() == 'labdev-nomad':
py = '/labEnv3/bin/python'
args = [py, 'main.py', '--annotate']
args.append(testfile)
print(' '.join(args))
proc = Popen(args, stdout=PIPE)
txt = proc.stdout.read()
with open('%s.json' % testfile, 'w') as fd:
......
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