From b7cccee8783cd3a763aa76f4352fae32ca429ec1 Mon Sep 17 00:00:00 2001
From: Ask Hjorth Larsen <asklarsen@gmail.com>
Date: Wed, 12 Oct 2016 20:41:38 +0200
Subject: [PATCH] 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.
---
parser/parser-molcas/main.py | 200 +++++++++++++++++++++++++------
parser/parser-molcas/runtests.py | 4 +-
2 files changed, 168 insertions(+), 36 deletions(-)
diff --git a/parser/parser-molcas/main.py b/parser/parser-molcas/main.py
index 3bd017c..ff980f0 100755
--- a/parser/parser-molcas/main.py
+++ b/parser/parser-molcas/main.py
@@ -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
diff --git a/parser/parser-molcas/runtests.py b/parser/parser-molcas/runtests.py
index 23b4d4b..7e18fc2 100755
--- a/parser/parser-molcas/runtests.py
+++ b/parser/parser-molcas/runtests.py
@@ -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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