setup.directorymaker(logger, targetdir)
setup.directorymaker(logger, '{0}{1}/'.format(targetdir, 'fullpostfiles'))
setup.directorymaker(logger, '{0}{1}/'.format(targetdir, 'truncpostfiles'))
#####First we'll calculate your isotherm and write a pressure.dat file in your target directory
satP = setup.pSat(logger, species[-1], T)
istm = setup.isothermcalculator(logger, satP, iso_length, minrelpress, maxrelpress)
setup.PressureFileWriter(logger, species[-1], T, satP, istm, targetdir) #goes in the directory above your individual one, gets symbolic linked later
##### Now to make some control files for you
setup.GcmcControlChanger(logger, species[-1], sorb_el_list, T, n, framework, '{0}'.format(targetdir), n_iterations, restart, ctrl_file_name, pressure)
for i, value in enumerate(istm): #now I make the extra .ctr files to give you final .xyz files for each simulaiton
setup.GcmcControlChanger(logger, species[-1], sorb_el_list, T, '1', framework, '{0}'.format(targetdir), '1', 'RESTARTFILE {0}.{1}.res.{2}'.format(framework, species[-1], i+1), '{0}kpa_restart.ctr'.format(value), value) #makes your control files for all of your pressure points
setup.PostControlChanger(logger, species[-1], T, n, framework, '{0}'.format(targetdir), '0')
setup.PostControlChanger(logger, species[-1], T, n, framework, '{0}'.format(targetdir), '60')
setup.GcmcRunWriter(logger, species[-1], T, framework, parentdir, '{0}'.format(targetdir), istm, '')#the last variable is the relative location of your interactions files
setup.AtmAtmMover(logger, sorb_el_list, forcefield, coultype, hicut, frameowrk, targetdir)
setup.SorbSorbWriter(logger, species[-1], sorb_el_list,framework,targetdir, pmap, emap)
setup.IntraWriter(logger, species[-1], sorb_el_list, framework, targetdir)
logger.info('''
##################################################################
So I've done the following:
Created the directory {0} which will run your simulation.
Calculated and written an isotherm between {1} and {2} kPa, then placed in it in {0}.
Created a gcmc.ctr file, 2 post control files, and a run.gcmc in {0}.
Finally I wrote an atom_atom_file, sorb_sorb_file, and intramolecular_file into {0}.
You're good to go!
##################################################################
'''.format(targetdir, satP*10**minrelpress, satP*10**maxrelpress))
satP = setup.pSat(logger, species[i], T)
istm = setup.isothermcalculator(logger, satP, iso_length, minrelpress, maxrelpress)
setup.PressureFileWriter(logger, species[i], T, satP, istm, '{0}{1:02d}/'.format(targetdir, j)) #goes in the directory above your individual one, gets symbolic linked later
workingdir += n_per_species
##### Now to make some control files for you
workingdir = 1
for i in range(1, n_species+1):
for directory in range(workingdir, workingdir+n_per_species):
setup.GcmcControlChanger(logger, species[i], sorb_el_list, T, n, framework, '{0}{1:02d}/'.format(targetdir, directory), n_iterations, restart, ctrl_file_name, pressure)
for j, value in enumerate(istm): #now I make the extra .ctr files to give you final .xyz files for each simulaiton
setup.GcmcControlChanger(logger, species[i], sorb_el_list, T, '1', framework, '{0}{1:02d}/'.format(targetdir, directory), '1', 'RESTARTFILE {0}.{1}.res.{2}'.format(framework, species[-1], j+1), '{0}kpa_restart.ctr'.format(value), value) #makes your control files for all of your pressure points
setup.PostControlChanger(logger, species[i], T, n, framework, '{0}{1:02d}/'.format(targetdir, directory), '0')
setup.PostControlChanger(logger, species[i], T, n, framework, '{0}{1:02d}/'.format(targetdir, directory), '60')
setup.GcmcRunWriter(logger, species[i], T, framework, parentdir, '{0}{1:02d}/'.format(targetdir, directory), istm, '')#the last variable is the relative location of your interactions files
setup.AtmAtmMover(logger, sorb_el_list, forcefield, coultype, hicut, frameowrk, '{0}{1:02d}/'.format(targetdir, directory))
setup.SorbSorbWriter(logger, species[i], sorb_el_list,framework,'{0}{1:02d}/'.format(targetdir, directory), pmap, emap)
setup.IntraWriter(logger, species[i], sorb_el_list, framework, '{0}{1:02d}/'.format(targetdir, directory))
setup.TaskfarmRunWriter(logger, 'multiple', T, framework, parentdir, targetdir, Taskfarm_total)
logger.info('''
##################################################################
So I've done the following:
Created the directory {0} and {1} subdirectories for taskfarming.
Calculated and written isotherms for all {2} species you've got, {3} times over each.
Created a gcmc.ctr file, 2 post control files, and a run.gcmc file for each subdirectory.
Created a taskfarm document and a backup, and finally run.taskfarmer in {0}. It might complain about not having a python script, but don't worry about that.
Finally I wrote an atom_atom_file, sorb_sorb_file, and intramolecular_file into each subdirectory.
You're good to go!
line.split()
) == 8: #should be 8 (index x y z name charge ? ?), but you might have added comments
logger.info(line.split()[4])
el_list.add(line.split()[4])
logger.info("Atom list found is: " + str(el_list))
else:
logger.warning(
'I didn\'t find a file named {0}.mol, so I don\'t have any sorbent atoms to write!'
.format(species))
sorb_el_list = [
] #i want to differentiate between framework elements and sorbent elements here, so I rename them as X_s
for i in el_list:
sorb_el_list.append(
"{0}_{1}".format(i.split("_")[0], 's')
) #Sometimes I'll call them X_something esle to denote their forcefield for instance. This hould cut it back to just X_s
logger.info(
'The list of sorbent atoms I\'ve found are: {0}'.format(sorb_el_list))
################
###############
setup.AtmAtmMover(
logger, #this variablwe logs out to the one made by this file
sorb_el_list, #Your elements to be considered in the fluid
forcefield, #Your forcefield tag for these elements
coultype, #Your fluid-fluid coulombic interaction model
cutoff, #Your nonbonded interaction cutoff distance
framework, #Your framework name, to look up in musicpy.Forcefield.MOF_el_list
targetdir #Where the atom_atom_interaction file will be spit out to
)