atoms_list=[]
collected_data={}
try:
for i in atoms_list1:
atoms_list.append(i)
except TypeError:
atoms_list1=open(ATOMS_DATA_FILE,"r")
atoms_list2=atoms_list1.readline().strip().split(" ")[0]
atoms_list.append(int(atoms_list2))
atom_count1=1
total_atoms=len(atoms_list)
for j in range(START_CHKPT_NUMBER,END_CHKPT_NUMBER,INTERVAL_CHKPT_NUMBER):
k=("%08d" %(j))
CUR_LAMMPS_FILE = str(CUR_LAMMPS_FILE_PREFIX)+str(".")+str(k)+str(".dump")
cur_atoms = ganisetti_tools.get_atoms_info_from_lammps(CUR_LAMMPS_FILE)
output1=open(CUR_LAMMPS_FILE_PREFIX+str("_selected_atoms_from_all_files.")+str(k)+str(".atoms"),'w')
output1.write("# MSD processed file; ITEM: ATOMS id type x y z\n\n")
output1.write("%d atoms\n" %(total_atoms))
output1.write("%d bonds\n" %(total_atoms-len(atoms_list)))
output1.write("0 angles\n0 dihedrals\n0 impropers\n\n")
output1.write("10 atom types\n1 bond types\n\n")
output1.write("%lf %lf xlo xhi\n" %(cur_atoms.box[0][0],cur_atoms.box[0][1]))
output1.write("%lf %lf ylo yhi\n" %(cur_atoms.box[1][0],cur_atoms.box[1][1]))
output1.write("%lf %lf zlo zhi\n\n" %(cur_atoms.box[2][0],cur_atoms.box[2][1]))
output1.write("Atoms \n\n")
if j != START_CHKPT_NUMBER:
for i in collected_data.keys():
output1.write("%d %d %d 1.0 %lf %lf %lf \n" %(collected_data[i]["id"],collected_data[i]["molecule_id"],collected_data[i]["type"],collected_data[i]["posx"],collected_data[i]["posy"],collected_data[i]["posz"]))
print(
"************************************** S. Ganisetti **************************************"
)
print("Error: usage is wrong")
print(
"correct usage is: python3.6 this_program ChkptFile SelectedAtomsList"
)
print(
"******************************************************************************************"
)
exit()
LAMMPS_CHKPT_FILE = sys.argv[1]
SELECTED_ATOMS_FILE = sys.argv[2]
ganisetti_tools.get_ganisetti_tools_version()
ref_atoms = ganisetti_tools.get_atoms_info_from_lammps(LAMMPS_CHKPT_FILE)
selected_atoms1 = open(SELECTED_ATOMS_FILE)
selected_atoms = []
for line in selected_atoms1:
elements = line.strip().split()
for each_element in elements:
selected_atoms.append(each_element)
output1 = open(LAMMPS_CHKPT_FILE + str("_selectedatoms.atoms"), 'w')
ganisetti_tools.write_imd_header_custom_property(output1, ref_atoms.box,
"EMPTY")
for i in selected_atoms:
#print(ref_atoms.id[int(i)])
ganisetti_tools.write_imd_atom_custom_property(output1, int(i),
ref_atoms, 0)
MAX_NEIGHBOURS=8
MAX_ATOM_TYPES=8
# controlling parameter
file_format = "lammps"
voxel_length_parameter = 0.5 # for example Si-O bond length is 2.2 Ang, and you want to keep 5 voxels within the Si-O bond
# then the voxel_length_parameter you have to provide is 2.2/5 = 0.44
voxel_smoothing_parameter = 6 # if you want to search for neighboring atoms within a separation distance of 2.7 Ang
# then the voxel_smoothing_parameter you have to provide is int(2.7/voxel_length_parameter) = int(6.1364) = 6
# **************************************************************************************
# get the atoms information
if file_format == "imd":
config1 = ganisetti_tools.get_atoms_info_from_imd(IMD_FILE)
if file_format == "lammps":
config1 = ganisetti_tools.get_atoms_info_from_lammps(LAMMPS_DUMP_FILE)
# **************************************************************************************
# compute total atoms of each atom type
total_atoms_of_type_sym={}
tmp=config1.type.values()
tmp=list(tmp)
for i in atom_type_sym2num.keys():
total_atoms_of_type_sym[i]=tmp.count(atom_type_sym2num[i])
# **************************************************************************************
# computing nnl
config1_nnl = ganisetti_tools.compute_nnl(config1,rc,atom_type_num2sym)
#all_clustering_required_atoms=[1759,586,383,524,237,2649,363,465,93,1868]
temp1 = atom_type_sym2num.keys()
BG_glass = "no"
if "Si" in temp1 and "P" in temp1 and "Na" in temp1 and "Ca" in temp1:
BG_glass = "yes"
NAPS_glass = "no"
if "P" in temp1 and "Al" in temp1 and "Na" in temp1:
NAPS_glass = "yes"
CMAS_glass = "no"
if "Ca" in temp1 and "Mg" in temp1 and "Al" in temp1 and "Si" in temp1:
CMAS_glass = "yes"
# main loop starts here
BASE_FILE = str(read_parameter_file.cur_file)
# **************************************************************************************
# get the atoms information
ref_config = ganisetti_tools.get_atoms_info_from_lammps(
read_parameter_file.input_lammps_dump_file)
cur_config = ganisetti_tools.get_atoms_info_from_lammps(
read_parameter_file.cur_lammps_dump_file)
MAX_ATOM_TYPE = max(ref_config.type.values())
# **************************************************************************************
# compute total atoms of each atom type
total_atoms_of_type_sym = {}
tmp = ref_config.type.values()
tmp = list(tmp)
for i in atom_type_sym2num.keys():
total_atoms_of_type_sym[i] = tmp.count(atom_type_sym2num[i])
# **************************************************************************************
# computing nnl
ref_config_nnl = ganisetti_tools.compute_nnl(ref_config, rc,
