'mol%i' % new_mol_number] = inputData[section][mol]
return newRestartData, newInputData
from MCFlow.file_formatting.writer import sort_keys
from MCFlow.file_formatting import reader, writer
if __name__ == '__main__':
from MCFlow.parser import ChangeInput
my_parser = ChangeInput()
my_parser.molecules()
my_parser.parser.add_argument('-b',
'--boxes',
help='boxes to keep',
type=str,
nargs='+')
args = vars(my_parser.parse_args())
for feed in args['feeds']:
for sim in args['indep']:
path = feed + '/' + str(sim) + '/'
input_data = reader.read_fort4(path + args['input'])
nmolty, nbox = int(input_data['&mc_shared']['nmolty']), int(
input_data['&mc_shared']['nbox'])
restart_data = reader.read_restart(path + args['restart'], nmolty,
nbox)
newRes, newIn = removeExtraInfo(args['boxes'], restart_data,
input_data)
writer.write_fort4(newIn, path + 'fort.4.purified')
writer.write_restart(newRes, path + 'fort.77.purified')
from MCFlow.file_formatting import reader, writer
import copy
import numpy as np
if __name__ == '__main__':
import argparse, os
parser = argparse.ArgumentParser(description='add explicit to unit cell')
parser.add_argument('-f', '--file', type=str)
parser.add_argument('-lmn',
'--vectors',
type=int,
nargs='+',
default=[2, 2, 3])
parser.add_argument('-i', '--input', default='fort.4')
parser.add_argument('-r', '--restart', default='fort.77')
args = vars(parser.parse_args())
base_dir = os.getcwd() + '/'
data = reader.PDB(args['file'])
input_data = reader.read_fort4('%s%s' % (base_dir, args['input']))
nmolty, nbox = (int(input_data['&mc_shared']['nmolty']),
int(input_data['&mc_shared']['nbox']))
restart_data = reader.read_restart('%s%s' % (base_dir, args['restart']),
nmolty, nbox)
input_data, restart_data = main(input_data, restart_data, data)
writer.write_fort4(input_data, 'fort.4.new')
writer.write_restart(restart_data, 'fort.77.new')
nargs='+')
my_parser.parser.add_argument('-ib',
'--impurityBoxes',
help='impurity boxes',
type=str,
nargs='+')
args = vars(my_parser.parser.parse_args())
feeds = args.pop('feeds')
for feed in feeds:
args['feeds'] = [feed]
data, gen_data = getFileData(**args)
nbox = len(data['rho'].averages[feed].keys())
try:
input_data = reader.read_fort4(args['path'] + '/' + feed +
'/1/fort.4')
except FileNotFoundError:
input_data = reader.read_fort4(args['path'] + '/' + feed +
'/1/old-fort4')
bias = newBias(data['N'].averages[feed],
input_data['UNIFORM_BIASING_POTENTIALS'],
gen_data[feed]['temperature'], args['impurityMols'],
args['impurityBoxes'])
# change data
input_data['UNIFORM_BIASING_POTENTIALS'] = bias
input_data['&mc_shared']['nstep'] = '%i' % args['nstep']
# iprint, iblock = iaverage(args['nstep'])
# input_data['&analysis']['iprint'] = '%i'%iprint
# input_data['&analysis']['iblock'] = '%i'%iblock
# write new files
if __name__ == '__main__':
import argparse, os
parser = argparse.ArgumentParser(description = 'Analyze and collect data for vapor adsorption')
parser.add_argument('-f','--in_file',help ='fort.4 file to change',type=str,
default=os.getcwd() + '/fort.4')
parser.add_argument('-r','--in_rest',help ='fort.77 file to change',type=str,
default=os.getcwd() + '/fort.77')
parser.add_argument('-b','--new_beads',help ='''new beads for each molecule type:
New order is lists for each mol. Ex: you might pass in `4,6,1,2,3,5' to get --> [4,6,1,2,3,5]. This changes
4 --> 1 (old bead 4 to new bead 1), 6 --> 2, 1 --> 3, etc...N.B: mols are read in string as list''',type=str,nargs='+')
parser.add_argument('-m','--mols',help='mols to change coresponding to those passed into new beads', type=str,nargs='+')
args = vars(parser.parse_args())
if len(args['new_beads']) != len(args['mols']):
print('beads and mols not specified correctly')
for key in ['new_beads','mols']:
print('{} {} len: {}'.format(key, args[key], len(args[key])))
quit()
new_beads = [list(map(int,i.split(','))) for i in args['new_beads']]
input_data = read_fort4(args['in_file'])
nmolty, nbox = int(input_data['&mc_shared']['nmolty']), int(input_data['&mc_shared']['nbox'])
restart_data = read_restart(args['in_rest'],nmolty, nbox)
new_in, new_res = changeBeadOrder(args['mols'], new_beads, input_data.copy(), restart_data.copy())
if args['in_file'].rfind('/') != -1:
new_path = args['in_file'][:args['in_file'].rfind('/')] + '/'
else:
new_path = ''
write_fort4(new_in, new_path + 'fort.4.new')
write_restart(new_res, new_path + 'fort.77.new')
newSwaps, newSwatches, pctAct, nActCycle, normSwaps,
normSwatches, pmvol, pswatch_norm, pswap_norm
) = analyzeTransfers(
data['SWAP'].averages[feed],
gen_data[feed]['ncycle'],
# nActPerCycle=3656/200, tavol=0.3,
gen_data[feed]['compositions'])
except NoSwapsAccepted:
print('no swaps accepted for {}'.format(feed))
continue
print(newSwaps)
# read and write
for sim in args['indep']:
my_path = '%s/%s/%i/' % (args['path'], feed, sim)
try:
input_data = reader.read_fort4(my_path + 'fort.4')
except FileNotFoundError:
input_data = reader.read_fort4(my_path + 'old-fort4')
# add in swaps
if input_data['&mc_swap']['pmswap'][-2:] == 'd0':
input_data['&mc_swap']['pmswap'] = input_data['&mc_swap'][
'pmswap'][:-2]
pswap_old = float(input_data['&mc_swap']['pmswap'])
input_data['&mc_swap']['pmswap'] = '%e' % pswap_norm
input_data['&mc_shared']['seed'] = '%i' % sim
nmolty = int(input_data['&mc_shared']['nmolty'])
assert len(newSwaps) == nmolty, 'Incorrect swaps: too many'
total_pswap = 0.
for molNum in range(1, nmolty + 1):
for mol in newSwaps.keys():
if mol.split()[0] == '%i' % molNum: