def Write_SimData(self, file):
uf.replace_text(file, "MOFNAME", self.mof_name)
uf.replace_text(file, "DDD1", self.box_0_vector1)
uf.replace_text(file, "DDD2", self.box_0_vector2)
uf.replace_text(file, "DDD3", self.box_0_vector3)
uf.replace_text(file, "BASEFUGACITY", self.mof_name[:4] + " 0.0")
self.sys.Write_Conf(file)
self.sim.Write_Conf(file)
def WriteXYZ(self, top_file):
''' Writing XYZ data calculated extension. and create Topology file'''
# detect the tag in cif file
cif_data = topGen.TopGenerate(self.cif_file)
cif_data.DetectTag()
cif_data.ReadCharges()
#create the topology with extension
topGen.MakeTopology(cif_data, top_file,
self.extend[0] * self.extend[1] * self.extend[2])
#Reading cif file
reachedAtom = False
molCount = 0
with open(self.output_file, 'w') as outfile:
outfile.write("TOTALATOM\n")
outfile.write(self.mof_name + "\n")
with open(self.cif_file, 'r') as infile:
for line in infile:
line = re.sub(' +', ' ', line).strip()
if line.startswith(cif_data.startTag):
reachedAtom = True
continue
if (reachedAtom):
if (line.startswith(cif_data.endTag)):
break
atom_name = line.split(' ')[cif_data.tag_symbol_indx]
x = float(line.split(' ')[cif_data.tag_x_indx])
y = float(line.split(' ')[cif_data.tag_y_indx])
z = float(line.split(' ')[cif_data.tag_z_indx])
if (cif_data.hasCharge):
charge = float(
line.split(' ')[cif_data.tag_charge_indx])
else:
charge = 0.0
atom_name = cif_data.GetAtomName(atom_name, charge)
frac_coord = np.array([x, y, z])
for i in range(self.extend[0]):
for j in range(self.extend[1]):
for k in range(self.extend[2]):
coord = self.cellBasis.Extend(
frac_coord, i, j, k)
to_print = "%4s %15.6f %15.6f %15.6f\n" % (
atom_name, coord[0], coord[1],
coord[2])
outfile.write(to_print)
molCount += 1
uf.replace_text(self.output_file, "TOTALATOM", str(molCount))
# Copy MOF cif file into MOF_base directory and set up the cell basis info and extension using
# maximum(rcut and rcutcoulomb)
print("Reading cell basis information in " + mof_file)
uf.Copy(mof_path, "./" + mof_file)
mof_cellBasis = euc.MOF_Data(mof_file, mof_name, conf.GetRcut())
conf.Print_cellData(mof_cellBasis)
# Create MOF Base
print("\n1. Building MOF files")
uf.Copy(base_directory + "/BUILD/pack/convert_XYZ_PDB.tcl",
"./convert_XYZ_PDB.tcl")
uf.Copy(base_directory + "/BUILD/model/" + top_file_adsorbent,
"./" + top_file_adsorbent)
#Prepare the Tcl script
uf.replace_text('convert_XYZ_PDB.tcl', 'MOFNAME', mof_name)
uf.replace_text('convert_XYZ_PDB.tcl', 'TOPFILENAME', top_file_adsorbent)
print(
"\t1. Extending unit cell and generating Topology and XYZ file for MOF."
)
mof_cellBasis.WriteXYZ(top_file_adsorbent)
if os.path.isfile(mof_name + ".xyz"):
print("\t2. Unit cell extended and XYZ file generated successfully.")
else:
print("\t2. ERROR: error generating supercell XYZ file.")
sys.exit(-1)
print("\t3. Converting XYZ file to PDB and PSF for MOF.")
os.system("vmd -dispdev text < convert_XYZ_PDB.tcl" +
'>> build_error.log 2>&1')
def Write_Conf(self, file):
''' Replace the keyword with value in config file'''
for i in range(len(self.simData)):
uf.replace_text(file, self.simData[i][1], self.simData[i][2])
def Write_Conf(self, file):
uf.replace_text(file, "ADSBNAME", self.adsorbate_name)
uf.replace_text(file, "FFIELD", self.model)
uf.replace_text(file, "DDD0", self.reservoir_dim)
uf.replace_text(file, "ADSBSET", self.adsorbate_resname)
def Write_runData(self, file, runID, dir):
self.runSim.Write_Conf(file, runID)
uf.replace_text("gcmc_cluster.cmd", "RUN-DIR", dir)
uf.replace_text("gcmc_cluster.cmd", "MOFNAME", self.mof_name)
uf.replace_text("gcmc_cluster.cmd", "ADSBNAME", self.sys.adsorbate_name)
uf.replace_text("gcmc_cluster.cmd", "FFF", self.runSim.FindVal(runID, 'fugacity'))
def Write_Conf(self, file, idx):
''' Replace the keyword with value in config file'''
for j in range(len(self.runSimData[idx][1])):
uf.replace_text(file, self.runSimData[idx][1][j][1], self.runSimData[idx][1][j][2])