##################################################################
## (c) Copyright 2015- by Jaron T. Krogel ##
##################################################################
#====================================================================#
# gamess.py #
# Nexus interface to the GAMESS simulation code. #
# #
# Content summary: #
# GamessInput #
# Input class for the GAMESS code. #
# Capable of reading/writing arbitrary GAMESS input files. #
# #
# generate_gamess_input #
# User function to create arbitrary GAMESS input. #
# #
# KeywordGroup #
# Represents an arbitrary keyword group in the input file. #
# #
# KeywordSpecGroup #
# Base class for specialized keyword groups. #
# Derived classes enforce the keyword specification. #
# See ContrlGroup, SystemGroup, GuessGroup, ScfGroup, #
# McscfGroup, DftGroup, GugdiaGroup, DrtGroup, CidrtGroup, #
# and DetGroup #
# #
# FormattedGroup #
# Represents strict machine-formatted input groups. #
# #
#====================================================================#
import os
import numpy as np
from .developer import obj
from .simulation import Simulation
from .gamess_input import GamessInput, generate_gamess_input, FormattedGroup, GuessGroup, GIarray
from .gamess_analyzer import GamessAnalyzer
[docs]
class Gamess(Simulation):
input_type = GamessInput
analyzer_type = GamessAnalyzer
generic_identifier = 'gamess'
application = 'gamess.x'
infile_extension = '.inp'
application_properties = set(['serial','mpi'])
application_results = set(['orbitals'])
ericfmt = None
mcppath = None
[docs]
@staticmethod
def settings(ericfmt=None,mcppath=None):
Gamess.ericfmt = ericfmt
Gamess.mcppath = mcppath
#end def settings
[docs]
@staticmethod
def restore_default_settings():
Gamess.ericfmt = None
Gamess.mcppath = None
#end def restore_default_settings
def __init__(self,**kwargs):
self.mo_reorder = None
mo_reorder = kwargs.pop('mo_reorder',None)
if mo_reorder is not None:
self.mo_reorder = [s.lower() for s in mo_reorder]
#end if
Simulation.__init__(self,**kwargs)
#end def __init__
#end def init_job_extra
[docs]
def check_result(self,result_name,sim):
input = self.input
if result_name=='orbitals':
calculating_result = 'contrl' in input and 'scftyp' in input.contrl and input.contrl.scftyp.lower() in ('rhf','rohf','uhf','mcscf','none')
else:
calculating_result = False
#end if
return calculating_result
#end def check_result
[docs]
def get_result(self,result_name,sim):
result = obj()
input = self.input
analyzer = self.load_analyzer_image()
if result_name=='orbitals':
result.location = os.path.join(self.locdir,self.outfile)
result.outfile = result.location
result.vec = None # vec from punch
result.norbitals = 0 # orbital count in punch
result.mos = 0 # orbital count (MO's) from log file
result.scftyp = input.contrl.scftyp.lower()
if 'counts' in analyzer and 'mos' in analyzer.counts:
result.mos = analyzer.counts.mos
#end if
if 'punch' in analyzer and 'vec' in analyzer.punch:
result.norbitals = analyzer.punch.norbitals
result.vec = analyzer.punch.vec
#end if
if 'orbitals' in analyzer:
result.orbitals = analyzer.orbitals
#end if
else:
self.error('ability to get result '+result_name+' has not been implemented')
#end if
return result
#end def get_result
[docs]
def incorporate_result(self,result_name,result,sim):
input = self.input
if result_name=='orbitals':
if result.vec is None or result.norbitals<1:
self.error('could not obtain orbitals from previous GAMESS run')
#end if
if 'guess' not in input:
input.guess = GuessGroup()
#end if
if 'norb' in input.guess: # user provided norb
norb = input.guess.norb
else:
norb = result.norbitals
#end if
if 'norder' not in input.guess:
input.guess.clear()
#end if
if self.mo_reorder is not None:
if 'orbitals' not in result:
self.error('Orbital information from prior calculation "{}" located at {} cannot be found. You requested orbital reordering via the "mo_reorder" input keyword. Due to missing information, this operation cannot be performed. The current simulation "{}" is located at {}.'.format(sim.identifier,sim.locdir,self.identifier,self.locdir))
self.block()
#end if
guess_inputs = obj()
ecounts = self.system.particles.electron_counts()
orbs = result.orbitals
order_map = obj(up='iorder',down='jorder')
nelec_map = obj(up=ecounts[0],down=ecounts[1])
for spin,vname in order_map.items():
nelec = nelec_map[spin]
if len(self.mo_reorder)<nelec:
self.error('Too few symmetries provided in "mo_reorder" for spin "{0}".\nNumber of electrons with spin "{0}": {1}\nNumber of entries in "mo_reorder": {2}\nContents of "mo_reorder": {3}\nSimulation identifier: {4}\nSimulation location: {5}'.format(spin,nelec,len(self.mo_reorder),self.mo_reorder,self.identifier,self.locdir))
#end if
symmetries = [s.lower() for s in orbs[spin].symmetry]
missing = set(self.mo_reorder)-set(symmetries)
if len(missing)>0:
self.error('Symmetries provided by "mo_reorder" keyword are not found in the outputted MOs.\nSet of symmetries provided in "mo_reorder": {}\nSet of symmetries present in MOs: {}\nContents of "mo_reorder": {}\nSimulation identifier: {}\nSimulation location: {}'.format(sorted(set(self.mo_reorder)),sorted(set(symmetries)),self.mo_reorder,self.identifier,self.locdir))
#end if
occ = np.zeros(len(symmetries),dtype=bool)
for symm in self.mo_reorder[:nelec]:
for i,(s,o) in enumerate(zip(symmetries,occ)):
if not o and symm==s:
occ[i] = True
break
#end if
#end for
#end for
if occ.sum()<nelec:
self.error('Too few orbitals occupied based on "mo_reorder" request.\nNumber of orbitals occupied: {}\nNumber of spin "{}" electrons: {}\nContents of "mo_reorder": {}\nSimulation identifier: {}\nSimulation location: {}'.format(occ.sum(),spin,nelec,self.mo_reorder,self.identifier,self.locdir))
#end if
indices = np.arange(len(symmetries),dtype=int)[occ]+1
start = 0
found = False
for i in range(len(indices)):
start = i
if indices[i]!=i+1:
found = True
break
#end if
#end if
if found:
reduced_indices = indices[start:]
start+=1
else:
reduced_indices = []
#end if
if len(reduced_indices)>0:
guess_inputs.norder = 1
guess_inputs[vname] = GIarray({start:reduced_indices})
#end if
#end for
input.guess.set(**guess_inputs)
#end if
input.guess.set(
guess = 'moread',
norb = norb,
prtmo = True,
)
input.vec = FormattedGroup(result.vec)
else:
self.error('ability to incorporate result '+result_name+' has not been implemented')
#end if
#end def incorporate_result
[docs]
def app_command(self):
if self.app_name == 'rungms':
return 'rungms '+self.infile
else:
return self.app_name+' '+self.infile.replace('.inp','')
#end if
#end def app_command
[docs]
def check_sim_status(self):
with open(os.path.join(self.locdir,self.outfile), "r") as out:
output = out.read()
#errors = open(os.path.join(self.locdir,self.errfile),'r').read()
self.failed = 'EXECUTION OF GAMESS TERMINATED -ABNORMALLY-' in output
self.finished = self.failed or 'EXECUTION OF GAMESS TERMINATED NORMALLY' in output
#end def check_sim_status
[docs]
def get_output_files(self):
output_files = []
return output_files
#end def get_output_files
[docs]
def output_filename(self,name):
name = name.upper()
if name not in GamessInput.file_units:
self.error('gamess does not produce a file matching the requested description: {0}'.format(name))
#end if
unit = GamessInput.file_units[name]
filename = '{0}.F{1}'.format(self.identifier,str(unit).zfill(2))
return filename
#end def output_filename
[docs]
def output_filepath(self,name):
filename = self.output_filename(name)
filepath = os.path.join(self.locdir,filename)
filepath = os.path.abspath(filepath)
return filepath
#end def
#end class Gamess
[docs]
def generate_gamess(**kwargs):
sim_args,inp_args = Gamess.separate_inputs(kwargs,copy_pseudos=False,sim_kw=['mo_reorder'])
if 'input' not in sim_args:
sim_args.input = generate_gamess_input(**inp_args)
#end if
gamess = Gamess(**sim_args)
return gamess
#end def generate_gamess
