def calcConductivity(self, molcharges, trjfilename, logfilename,
datfilename, T, output):
lrun = LammpsRun(datfilename, trjfilename, logfilename)
dt = lrun.timestep
tsjump = lrun.jump(trjfilename)
(num_lines, n, num_timesteps, count, line) = self.getnum(trjfilename)
atommass = self.getmass(datfilename)
V = self.getdimensions(trjfilename[0])
(vx, vy, vz, mol, atype, j, J) = self.createarrays(n, num_timesteps)
(vxcol, vycol, vzcol, idcol, molcol,
typecol) = self.getcolumns(trjfilename[0])
for i in range(0, len(trjfilename)):
trjfile = open(trjfilename[i])
while line[i] < num_lines[i]:
(vx, vy, vz, line, mol,
atype) = self.readdata(trjfile, n, line, vx, vy, vz, vxcol,
vycol, vzcol, idcol, i, mol, molcol,
atype, typecol)
if count == 0:
(comvx, comvy, comvz, nummol,
molmass) = self.COMprep(mol, atype, atommass, n)
(comvx, comvy,
comvz) = self.calcCOMv(comvx, comvy, comvz, vx, vy, vz, mol,
atype, atommass, molmass, n, nummol)
(j, count) = self.calcj(molcharges, comvx, comvy, comvz, j,
count)
J = self.clacJ(j, J)
integral = self.integrateJ(J, tsjump * dt)
time = []
for i in range(0, len(integral)):
time.append(i * tsjump * dt)
popt = self.fitcurve(time, integral)
cond = self.greenkubo(popt, T, V)
output['Conductivity']['Green_Kubo'] = cond
file = open('integral.dat', 'w')
for i in range(0, len(integral)):
file.write(str(integral[i]) + '\n')
return output
def test_other():
"""
Sample driver file to calculate the MSD and diffusivity for all
molecules in a system as well as the center of mass radial distribution
function for all pairs of molecules in the system. Will also integrate
the rdf to get the coordination number and calculate the ion pair lifetime
for the system
Requires the following comments in the lammps data file starting
at the third line
# 'number' 'molecule' molecules
where 'number' is the number of that molecule type and
'molecule' is a name for that molecule
Do not include blank lines in between the molecule types
Outputs are stored in a dictionary called output to later be stored
in JSON format
"""
trjfilename = [
os.path.join(MODULE_DIR, 'tests/sample_files/NaSCN.lammpstrj')
]
datfilename = os.path.join(MODULE_DIR,
'tests/sample_files/data.water_1NaSCN')
logfilename = os.path.join(MODULE_DIR, 'tests/sample_files/mol.log')
lrun = LammpsRun(datfilename, trjfilename, logfilename)
c = CenterOfMass()
m = MeanSquareDisplacement()
crd = RadialDistributionPure()
ne = NernstEinsteinConductivity()
cn = CoordinationNumber()
ip = IonPair()
output = {}
output['RDF'] = {}
output['RDF']['units'] = 'unitless and angstroms'
output['Conductivity'] = {}
output['Conductivity']['units'] = 'S/m'
T = 298 # get from lammpsio
tsjump = lrun.jump()
(nummoltype, moltypel, moltype) = lrun.get_mols()
dt = lrun.timestep
n = lrun.natoms()
(molcharges, atomcharges, n) = lrun.get_mol_charges(n)
molcharge = lrun.get_mol_charge_dict(molcharges, moltypel, moltype)
(comx, comy, comz, Lx, Ly, Lz, Lx2, Ly2,
Lz2) = c.calcCOM(trjfilename, datfilename)
output = m.runMSD(comx, comy, comz, Lx, Ly, Lz, Lx2, Ly2, Lz2, moltype,
moltypel, dt, tsjump, output)
output = ne.calcNEconductivity(output, molcharge, Lx, Ly, Lz, nummoltype,
moltypel, T)
ip.runionpair(comx,
comy,
comz,
Lx,
Ly,
Lz,
moltypel,
moltype,
tsjump,
dt,
output,
skipframes=0)
output = crd.runradial(datfilename,
comx,
comy,
comz,
Lx,
Ly,
Lz,
Lx2,
Ly2,
Lz2,
output,
nummoltype,
moltypel,
moltype,
firststep=1)
output = cn.compute(output, nummoltype, moltypel, Lx * Ly * Lz)
def lampps_properties(self, trjfile, datafile, logfile):
"""
calculate the MSD and diffusivity for all
molecules in a system as well as the center of mass radial distribution
function for all pairs of molecules in the system
Requires the following comments in the lammps data file starting
at the third line
# "number" "molecule" molecules
where "number" is the number of that molecule type and
"molecule" is a name for that molecule
Do not include blank lines in between the molecule types
Outputs are stored in a dictionary called output to later be stored
in JSON format
:return: Output
"""
lrun = LammpsRun(datafile, trjfile, logfile)
c = CenterOfMass()
m = MeanSquareDisplacement()
crd = RadialDistributionPure()
ne = NernstEinsteinConductivity()
output = {}
output['RDF'] = {}
output['RDF']['units'] = 'unitless and angstroms'
output['Conductivity'] = {}
output['Conductivity']['units'] = 'S/m'
T = 298 # get from lammpsio
tsjump = lrun.jump()
(nummoltype, moltypel, moltype) = lrun.get_mols()
dt = lrun.timestep
n = lrun.natoms()
(molcharges, atomcharges, n) = lrun.get_mol_charges(n)
molcharge = lrun.get_mol_charge_dict(molcharges, moltypel, moltype)
(comx, comy, comz, Lx, Ly, Lz, Lx2, Ly2, Lz2) = c.calcCOM([trjfile],
datafile)
output = m.runMSD(comx, comy, comz, Lx, Ly, Lz, Lx2, Ly2, Lz2, moltype,
moltypel, dt, tsjump, output)
output = ne.calcNEconductivity(output, molcharge, Lx, Ly, Lz,
nummoltype, moltypel, T)
output = crd.runradial(datafile,
comx,
comy,
comz,
Lx,
Ly,
Lz,
Lx2,
Ly2,
Lz2,
output,
nummoltype,
moltypel,
moltype,
firststep=1)
return output