def runscript(value=1):
if value == 0:
inp = createscript()
if value == 1:
inpufile = input('Input file name [inputnam.format]:')
with open(inpufile, 'r') as myfile:
inp = myfile.read()
if value == 0:
structurename = input('Input structure name (name.cif): ')
structur = structurename.split('.')
strc = next(pybel.readfile(structur[1], structurename))
strc.unitcell.FillUnitCell(strc.OBMol)
strc.calccharges("eqeq")
out = RASPA2.run_script(inp, strc)
if value == 1:
while value == 1:
structurename = input('Structure (Optional) [name.cif/None]: ')
if structurename == 'None':
value = 2
out = RASPA2.run_script(inp)
if structurename != 'None':
structur = structurename.split('.')
strc = next(pybel.readfile(structur[1], structurename))
strc.unitcell.FillUnitCell(strc.OBMol)
strc.calccharges("eqeq")
value = 2
out = RASPA2.run_script(inp, strc)
return out, inp
def getheliumvoidfraction():
print('Define the following parameter:')
print(
' *for default option, you must introduce the exactly default ex:CrystalGenerator'
)
print('')
structurename = input('Input structure name (name.cif): ')
structur = structurename.split('.')
strc = next(pybel.readfile(structur[1], structurename))
strc.unitcell.FillUnitCell(strc.OBMol)
strc.calccharges("eqeq")
unitcells = input('unit_cells [default=(1,1,1)]: ')
unitcells = unitcells.split(',')
a = unitcells[0]
a = a[1]
b = unitcells[1]
c = unitcells[2]
c = c[0]
cycles = int(input('cycles [default=2000]: '))
forcefield = input('forcefield [default=CrystalGenerator]: ')
voidfrac = RASPA2.get_helium_void_fraction(strc,
unit_cells=(a, b, c),
cycles=cycles,
input_file_type="cif",
forcefield=forcefield)
print('The helium void fraction is ' + str(voidfrac))
return voidfrac
def getgeometricsurfacearea():
print('Define the following parameter:')
print(
' *for default option, you must introduce the exactly default ex:CrystalGenerator'
)
print('')
structurename = input('Input structure name (name.cif): ')
structur = structurename.split('.')
strc = next(pybel.readfile(structur[1], structurename))
strc.unitcell.FillUnitCell(strc.OBMol)
strc.calccharges("eqeq")
unitcells = input('unit_cells [default=(1,1,1)]: ')
unitcells = unitcells.split(',')
a = unitcells[0]
a = a[1]
b = unitcells[1]
c = unitcells[2]
c = c[0]
cycles = int(input('cycles [default=500]: '))
forcefield = input('forcefield [default=CrystalGenerator]: ')
srfcarea = RASPA2.get_geometric_surface_area(strc,
unit_cells=(a, b, c),
cycles=cycles,
input_file_type="cif",
units="m^2/g",
forcefield=forcefield)
print('The geometric surface area=' + str(srfcarea) + 'm^2/g')
return srfcarea
def runmixture():
structurename = input('Input structure name (name.cif): ')
structur = structurename.split('.')
strc = next(pybel.readfile(structur[1], structurename))
strc.unitcell.FillUnitCell(strc.OBMol)
strc.calccharges("eqeq")
unitcells = input('unit_cells [default=(1,1,1)]: ')
unitcells = unitcells.split(',')
a = unitcells[0]
a = a[1]
b = unitcells[1]
c = unitcells[2]
c = c[0]
cycles = int(input('cycles [default=500]: '))
forcefield = input('forcefield [default=CrystalGenerator]: ')
simulationtype = input('Simulation type [default=MonteCarlo]: ')
print(
'Now you will be asked for the number ofdifferent molecules, their names and the mol fraction of each one [number of molecules and names introduce must match ]'
)
nummolecules = int(input('Number of molecules to test: '))
molecules = []
molfractions = []
control = 1
temperature = int(float(input('Temperature (K) [default=273.15]: ')))
pressure = int(float(input('Pressure (Pa) [default=101325]: ')))
while control == 1:
print('Want to calculate the helium void fraction or add it manully?')
des = input('[calculate/ manual [default=1.0]:')
if des != 'calculate' and des != 'manual':
continue
if des == 'calculate':
void = int(float(getheliumvoidfraction()))
if des == 'manual':
void = int(float(input('Value= ')))
for i in range(nummolecules):
mol = input('Molecule name [name]:')
molfr = int(float(input('Mol fraction: ')))
molecules.append(mol)
molfractions.append(molfr)
out = RASPA2.run_mixture(strc,
molecules=molecules,
mol_fractions=molfractions,
temperature=temperature,
pressure=pressure,
helium_void_fraction=void,
unit_cells=(a, b, c),
simulation_type=simulationtype,
cycles=cycles,
init_cycles="auto",
forcefield=forcefield,
input_file_type="cif")
return out
def raspa_task(args):
'''Task to compute provider side (RASPA specific).
It's possible to import RASPA2 package on remote side because
it's preinstalled in a docker environment we are about to use to
run this task. Every non standard package has to be installed
in the remote environment first.
'''
import RASPA2
import pybel
mol = pybel.readstring('cif', args['mol'])
return RASPA2.get_helium_void_fraction(mol)
def runn():
structurename = input('Input structure name (name.cif): ')
structur = structurename.split('.')
strc = next(pybel.readfile(structur[1], structurename))
strc.unitcell.FillUnitCell(strc.OBMol)
strc.calccharges("eqeq")
unitcells = input('unit_cells [default=(1,1,1)]: ')
unitcells = unitcells.split(',')
a = unitcells[0]
a = a[1]
b = unitcells[1]
c = unitcells[2]
c = c[0]
temperature = int(float(input('Temperature (K) [default=273.15]: ')))
presure = int(float(input('Pressure (Pa) [default=101325]: ')))
cycles = int(input('cycles [default=2000]: '))
forcefield = input('forcefield [default=CrystalGenerator]: ')
simulationtype = input('Simulation type [default=MonteCarlo]: ')
molecule = input('Molecule name [name]: ')
frameworkname = input('Framework name [default=streamed]')
control = 1
while control == 1:
print('Want to calculate the helium void fraction or add it manully?')
des = input('[calculate/ manual :')
if des != 'calculate' and des != 'manual':
continue
if des == 'calculate':
void = int(float(getheliumvoidfraction()))
control = 2
if des == 'manual':
void = int(float(input('Value [default=1.0]= ')))
control = 2
out = RASPA2.run(strc,
molecule,
temperature=temperature,
pressure=presure,
helium_void_fraction=void,
unit_cells=(a, b, c),
framework_name=frameworkname,
simulation_type=simulationtype,
cycles=cycles,
init_cycles="auto",
forcefield=forcefield,
input_file_type="cif")
return out
def getporesizedistribution():
print(
'Returns a list of the form [[x1, x2, ..., xn], [y1, y2, ..., yn]], where x is the binned pore size (in Angstroms) and y is the partial pore volume (in cm^3 / g).'
)
print('Define the following parameter:')
print(
' *for default option, you must introduce the exactly default ex:CrystalGenerator'
)
print('')
structurename = input('Input structure name (name.cif): ')
structur = structurename.split('.')
strc = next(pybel.readfile(structur[1], structurename))
strc.unitcell.FillUnitCell(strc.OBMol)
strc.calccharges("eqeq")
unitcells = input('unit_cells [default=(1,1,1)]: ')
unitcells = unitcells.split(',')
a = unitcells[0]
a = a[1]
b = unitcells[1]
c = unitcells[2]
c = c[0]
cycles = int(input('cycles [default=500]: '))
forcefield = input('forcefield [default=CrystalGenerator]: ')
bins = int(input('bin number of the histogram output [default=50]: '))
porsedistrib = RASPA2.get_pore_size_distribution(strc,
unit_cells=(a, b, c),
cycles=cycles,
input_file_type="cif",
forcefield=forcefield,
bins=bins)
x = porsedistrib[0]
y = porsedistrib[1]
mtplot.plot(x, y)
mtplot.xlabel('Binned pore size (Angstrom)')
mtplot.ylabel('Partial pore volume (cm^3 / g)')
mtplot.show()
return porsedistrib
def createscript():
molecule = input('Molecule name [name]: ')
unitcells = input('unit_cells [default=(1,1,1)]: ')
unitcells = unitcells.split(',')
a = unitcells[0]
a = a[1]
b = unitcells[1]
c = unitcells[2]
c = c[0]
temperature = int(float(input('Temperature (K) [default=273.15]: ')))
presure = int(float(input('Pressure (Pa) [default=101325]: ')))
cycles = int(input('cycles [default=2000]: '))
forcefield = input('forcefield [default=CrystalGenerator]: ')
simulationtype = input('Simulation type [default=MonteCarlo]: ')
control = 1
while control == 1:
print('Want to calculate the helium void fraction or add it manully?')
des = input('[calculate/ manual :')
if des != 'calculate' and des != 'manual':
continue
if des == 'calculate':
void = int(float(getheliumvoidfraction()))
control = 2
if des == 'manual':
void = int(float(input('Value [default=1.0]= ')))
control = 2
out = RASPA2.create_script(molecule,
temperature=temperature,
pressure=presure,
helium_void_fraction=void,
unit_cells=(a, b, c),
simulation_type=simulationtype,
cycles=cycles,
init_cycles="auto",
forcefield=forcefield,
input_file_type="cif")
return out
import RASPA2
input_script = RASPA2.create_script("H2",
temperature=298,
pressure=1000000,
helium_void_fraction=1.0,
input_file_type="cif")
print input_script
import pybel
import RASPA2
import pandas as pd
#import matplotlib.pyplot as plt
# Set up
gas = "H2"
#pressures = [1e4 * 10**(0.1 * i) for i in range(31)]
pressures = [3.5e7,7.0e7,10.0e7]
# Use pybel to parse, fill, and charge cif structure
my_structure = pybel.readfile("cif", "IRMOF-1.cif").next()
#my_structure.unitcell.FillUnitCell(mol.OBMol)
#my_structure.calccharges("eqeq")
# Run
results = [RASPA2.run(my_structure, gas, temperature=298, pressure=pressure) for pressure in pressures]
# Parse
uptakes = [r["Number of molecules"][gas]["Average loading absolute [cm^3 (STP)/cm^3 framework]"][0] for r in results]
# print
z = [pressures,uptakes]
df = pd.DataFrame(z).T
df.to_csv("Pa_vs_NumAbsGas.csv")
# Plot
#plt.plot(pressures, uptakes)
#plt.show()
def f(mof):
import RASPA2
output = RASPA2.run(mof["cif"], "H2", temperature=298, pressure=65e5, helium_void_fraction=mof["helium void fraction"], input_file_type="cif")
return output["Number of molecules"]["H2"]["Average loading absolute [milligram/gram framework]"][0]