Skip to content

Commit

Permalink
Added functionality to write data files for solid-liquid interface sy…
Browse files Browse the repository at this point in the history 
…stems
  • Loading branch information
@mmbliss
mmbliss committed Jul 11, 2024
1 parent d1306e4 commit 2de3f6b
Show file tree
Hide file tree
Showing 4 changed files with 202 additions and 45 deletions.
36 changes: 36 additions & 0 deletions pymatgen/core/bond_lengths.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -394,5 +394,41 @@
"H"
],
"bond_order": 1.0
},
{
"ref": "",
"length": 1.787,
"elements": [
"Al",
"O"
],
"bond_order": 1.0
},
{
"ref": "",
"length": 2.945,
"elements": [
"Al",
"C"
],
"bond_order": 0.0
},
{
"ref": "",
"length": 3.376,
"elements": [
"Al",
"F"
],
"bond_order": 0.0
},
{
"ref": "",
"length": 3.615,
"elements": [
"Al",
"H"
],
"bond_order": 0.0
}
]
190 changes: 151 additions & 39 deletions pymatgen/io/lammps/data.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -734,6 +734,11 @@ def from_ff_and_topologies(cls, box, ff, topologies, atom_style="full"):
"""
atom_types = set.union(*[t.species for t in topologies])
print(f"atom_types:\n{atom_types}\n")
print(f"ff object:\n{ff}\n")
print(f"ff.maps:\n{ff.maps}\n")
print(f"ff.maps['Atoms']:\n{ff.maps['Atoms']}\n")
print(f"ff.maps['Atoms'].keys():\n{ff.maps['Atoms'].keys()}\n")
assert atom_types.issubset(ff.maps["Atoms"].keys()), "Unknown atom type found in topologies"

items = dict(box=box, atom_style=atom_style, masses=ff.masses, force_field=ff.force_field)
Expand Down Expand Up @@ -1725,29 +1730,41 @@ def __init__(
length_increase=0.5,
check_ff_duplicates=True,
box_data_type="cubic",
system_molecule=None,
system_molecule_type=None,
sorted_mol_names=None,
):
"""
Low level constructor designed to work with lists of dictionaries that should
be able to be obtained from databases. Works for cubic boxes only using
real coordinates.
:param system_force_fields: [dict] Contains force field information using
the following format:
Low level constructor designed to work with lists of
dictionaries that should be able to be obtained from databases.
Works for cubic boxes only using real coordinates.
:param system_force_fields: [dict] Contains force field
information using the following format:
{ unique_molecule_name: {
'Molecule': pymatgen.Molecule,
'Labels': [atom_a, ...]
'Masses': [OrderedDict({species_1: mass_1, ...})],
'Nonbond': [[...], ...],
'Bonds': [{'coeffs': [...], 'types': [(i, j), ...]}, ...],
'Angles': [{'coeffs': [...], 'types': [(i, j, k), ...]}, ...],
'Dihedrals': [{'coeffs': [...], 'types': [(i, j, k, l), ...]}, ...],
'Impropers': [{'coeffs': [...], 'types': [(i, j, k, l), ...]}, ...],
'Bonds': [
{'coeffs': [...], 'types': [(i, j), ...]}, ...
],
'Angles': [
{'coeffs': [...], 'types': [(i, j, k), ...]}, ...
],
'Dihedrals': [
{'coeffs': [...], 'types': [(i, j, k, l), ...]}, ...
],
'Impropers': [
{'coeffs': [...], 'types': [(i, j, k, l), ...]}, ...
],
'Improper Topologies': [[a, b, c, d],...]
'Charges': [atom_a, ...]
}, ...}
:param system_mixture_data: [dict] Format depends on mixture_data_type input.
For mixture_data_type = 'concentration', this parameter contains molarity,
density, and molar weights of solutes and solvents using the
following format:
:param system_mixture_data: [dict] Format depends on
mixture_data_type input.
For mixture_data_type = 'concentration', this parameter
contains molarity, density, and molar weights of solutes and
solvents using the following format:
{
'Solutes': {unique_molecule_name: {
'Initial Molarity': molarity_1i,
Expand All @@ -1762,22 +1779,84 @@ def __init__(
'Molar Weight': molar_weight_1
}, ...}
}
For mixture_data_type = 'number of molecules', this parameter contains
the number of molecules for each species in the system in the following
format:
For mixture_data_type = 'number of molecules', this
parameter contains the number of molecules for each species
in the system in the following format:
{
unique_molecule_name: n_mols,
...
}
:param mixture_data_type: [str] controls the format of the system_mixture_data
parameter. Currently supports values of 'concentration' and
'number of molecules'. Defaults to "concentration".
:param cube_length: [float] length of system box in angstroms.
:param origin: [list] Optional. Change if the minimum xyz coordinates for
desired box are not [0,0,0].
:param box_data: [float, 3x2 array_like, LammpsBox] This
parameter controls the dimensions of the system box. The
format depends on the value of box_data_type.
For box_data_type = 'cubic', this parameter is a float and
sets the length of the cubic box.
For box_data_type = 'rectangular', this parameter is a 3x2
array_like and sets the bounds of the rectangular box.
For box_data_type = 'LammpsBox', this parameter is a pmg
LammpsBox object and sets the bounds of the box.
:param mixture_data_type: [str] controls the format of the
system_mixture_data parameter. Currently supports values of
'concentration', 'number of molecules', 'pmg molecule', and
'xyz'. Defaults to "concentration".
:param origin: [1x3 array_like] Optional. Change if the minimum
xyz coordinates for desired box are not [0,0,0].
:param seed: [int] Optional. Sets the seed for running packmol.
:param packmolrunner_inputs: [dict] Optional. Parameters for PackmolRunner
in pymatgen.io.lammps.utils
This parameter will update the 'seed' key in the
packmolrunner_inputs parameter. Defaults to 150.
:param packmolrunner_inputs: [dict] Optional. Parameters for
PackmolRunner in pymatgen.io.lammps.utils
:param length_increase: [float] Optional. Because packmol will
not always strictly adhere to the box dimensions, this
parameter sets the amount to increase the box dimensions by
in order to ensure that all molecules are within the box. It
will increase the length of the box by this amount in the x,
y, and z directions. In effect, it will decrease the min box
value by half of its value and increase the max box value by
half of its value Defaults to 0.5. This means that the min
values of x, y, and z will be decreased by 0.25 and the max
values of x, y, and z will be increased by 0.25 by default.
If using the default value, it might be advisable to set the
origin to [0.25, 0.25, 0.25] to ensure that the true box
origin is at [0,0,0].
:param check_ff_duplicates: [bool] Optional. If True, the angle,
dihedral, and improper bond types will be checked for
duplicates (eg, for angles, the following two types are
duplicates: ("C", "O", "H") and ("H", "O", "C")). If
duplicates are found, a warning will be issued. Defaults to
True.
:param box_data_type: [str] Optional. Controls the format of the
box_data parameter. Currently supports values of 'cubic',
'rectangular', and 'LammpsBox'. Defaults to "cubic".
:param system_molecule: [pmg Molecule, str] Optional. If
mixture_data_type is 'pmg molecule', this parameter should
contain a pmg Molecule object containing all of the
molecules in the system. The order of the molecules in this
object should be similar to that created by the
PackmolRunner object. That is, all sites belonging to the
first molecule should be listed first, then all sites
belonging to the second molecule, and so on. Also, the sites
belonging to each molecular species should be sorted such
that all the sites belonging to the first molecular species
occur first, then all the sites belonging to the second
molecular species, and so on.
If mixture_data_type is 'xyz', this parameter should contain
a path to an xyz file containing the coordinates of all the
molecules in the system. The order of the molecules in this
file should be similar to the xyz file created by the
PackmolRunner object, and by extension, the 'pmg molecule'
version of this parameter.
If this parameter is used, then the system_mixture_data
should be the number of molecules in the system.
If None, the system molecule will be created from packmol
based on the system_mixture_data. Defaults to None.
:param system_molecule_type: [str] Optional. controls the format
of the system_molecule parameter. Currently supports values
of 'pmg molecule' and 'xyz'. Defaults to None.
:param sorted_mol_names: [list] Optional. Contains the unique
molecule names in the system. If None, the molecule names
will be sorted from most to least number of atoms. Defaults
to None.
"""
self._ff_list = system_force_fields
self._concentration_data = False
Expand All @@ -1797,17 +1876,18 @@ def __init__(
elif mixture_data_type == "number of molecules":
self._number_of_molecules_data = True
self._n_mol_dict = system_mixture_data


self._origin = origin
if box_data_type == "cubic":
self.length = box_data
self._initial_lammps_box = LammpsBox([[0.0, box_data],
[0.0, box_data],
[0.0, box_data]])
self._initial_lammps_box = LammpsBox([[self._origin[0], box_data],
[self._origin[1], box_data],
[self._origin[2], box_data]])
elif box_data_type == "rectangular":
self._initial_lammps_box = LammpsBox(box_data)
elif box_data_type == "LammpsBox":
self._initial_lammps_box = box_data
self._origin = origin


packmolrunner_inputs["control_params"]["seed"] = seed
self._packmolrunner_inputs = packmolrunner_inputs
Expand All @@ -1818,19 +1898,48 @@ def __init__(
self._length_increase = length_increase
self._check_ff_duplicates = check_ff_duplicates

if system_molecule_type is None:
self._packmol_run_status = True
elif system_molecule_type in ["pmg molecule", "xyz"]:
self._packmol_run_status = False
if system_molecule_type == "xyz":
self._sys_molecule = Molecule.from_file(system_molecule)
else:
self._sys_molecule = system_molecule
if mixture_data_type != "number of molecules":
raise ValueError(
"The system_molecule_type parameter is not valid. \
Currently, the only valid value for this parameter is \
'number of molecules' if also using a system_molecule \
parameter."
)
else:
raise ValueError(
"The system_molecule_type parameter is not valid. Currently, \
the only valid values are 'pmg molecule' and 'xyz'."
)

self._sorted_mol_names = sorted_mol_names


@property
def sorted_mol_names(self):
"""
Sorts molecules from most to least number of atoms
:return molecule_name_list: [list] Contains the unique_molecule_names
Sorts molecules from most to least number of atoms. Only used if
sorted_mol_names is None.
:return molecule_name_list: [list] Contains the
unique_molecule_names
"""
molecule_name_list = list(self._ff_list.keys())
molecule_natoms_list = [len(self._ff_list[name]["Molecule"]) for
name in molecule_name_list]
molecule_name_list.sort(key=dict(zip(molecule_name_list,
molecule_natoms_list)).get,
reverse=True)
return molecule_name_list
if self._sorted_mol_names is not None:
return self._sorted_mol_names
else:
molecule_name_list = list(self._ff_list.keys())
molecule_natoms_list = [len(self._ff_list[name]["Molecule"]) for
name in molecule_name_list]
molecule_name_list.sort(key=dict(zip(molecule_name_list,
molecule_natoms_list)).get,
reverse=True)
return molecule_name_list

@property
def nmol_dict(self):
Expand Down Expand Up @@ -2072,7 +2181,10 @@ def _get_lammps_box(self, system_molecule):
return mix_lmpbox

def build_lammps_data(self, atom_style="full"):
system_molecule = self._run_packmol()
if self._packmol_run_status:
system_molecule = self._run_packmol()
else:
system_molecule = self._sys_molecule
system_topologies = self._get_topologies(system_molecule)
system_lammps_box = self._get_lammps_box(system_molecule)
system_lammps_data = LammpsData.from_ff_and_topologies(
Expand Down
10 changes: 5 additions & 5 deletions pymatgen/io/lammps/scripts/Dump_to_dumps_and_xyz.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
"""

cwd = os.getcwd()
dump_file_path_pattern = os.path.join(cwd, "dump.*.dump")
dump_file_path_pattern = os.path.join(cwd, "*.lammpstrj.2000000")

Dump_files = glob.glob(dump_file_path_pattern)

Expand All @@ -25,11 +25,11 @@
Dumps = parse_lammps_dumps(Dump_file)

for Dump in Dumps:
trj_name = Dump_file_name[:-4] + str(Dump.timestep) + ".lammpstrj"
# trj_name = Dump_file_name[:-4] + str(Dump.timestep) + ".lammpstrj"
xyz_name = Dump_file_name[:-4] + "alt." + str(Dump.timestep) + ".xyz"
Dump.as_txt_file(trj_name, output=True)
Dump.as_txt_file(xyz_name, convert="xyz", output=True)
if Dump.timestep % 500000 == 0:
run(["cp", trj_name, "trj_files/rdf_files"])
run(["mv", trj_name, "trj_files"])
# if Dump.timestep % 500000 == 0:
# run(["cp", trj_name, "trj_files/rdf_files"])
# run(["mv", trj_name, "trj_files"])
run(["mv", xyz_name, "xyz_files"])
11 changes: 10 additions & 1 deletion pymatgen/io/lammps/utils.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -188,6 +188,7 @@ def __init__(
filetype="xyz",
control_params={"maxit": 20, "nloop": 600},
auto_box=True,
origin=[0.0, 0.0, 0.0],
output_file="packed.xyz",
bin="packmol",
encode=False
Expand All @@ -209,6 +210,8 @@ def __init__(
list of parameters containing dicts for each molecule
auto_box:
put the molecule assembly in a box
origin:
coordinates for the origin of the box
output_file:
output file name. The extension will be adjusted
according to the filetype
Expand All @@ -229,6 +232,7 @@ def __init__(
self.param_list = param_list
self.input_file = input_file
self.boxit = auto_box
self.origin = origin
self.control_params = control_params
if not self.control_params.get("tolerance"):
self.control_params["tolerance"] = tolerance
Expand Down Expand Up @@ -266,7 +270,12 @@ def _set_box(self):
net_volume += (length ** 3.0) * float(self.param_list[idx]["number"])
length = net_volume ** (1.0 / 3.0)
for idx, mol in enumerate(self.mols):
self.param_list[idx]["inside box"] = "0.0 0.0 0.0 {} {} {}".format(length, length, length)
self.param_list[idx]["inside box"] = "{} {} {} {} {} {}".format(self.origin[0],
self.origin[1],
self.origin[2],
self.origin[0] + length,
self.origin[1] + length,
self.origin[2] + length)

def _write_input(self, input_dir="."):
"""
Expand Down

0 comments on commit 2de3f6b

Please sign in to comment.