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Controller n2p2 write #3

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Controller n2p2 write #3

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149 changes: 86 additions & 63 deletions src/cc_hdnnp/controller.py
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Original file line number Diff line number Diff line change
Expand Up @@ -386,10 +386,12 @@ def scale_xyz(
def write_cp2k(
self,
structure_name: str,
basis_set_directory: str,
potential_directory: str,
basis_set_dict: Dict[str, str],
potential_dict: Dict[str, str],
# basis_set_directory: str,
# potential_directory: str,
# basis_set_dict: Dict[str, str],
# potential_dict: Dict[str, str],
param_file_path: str = "DFTB_param/scc ",
param_file_name: str = "scc_parameter ",
file_bash: str = "all.sh",
file_batch: str = "{}.sh",
file_input: str = "cp2k_input/{}.inp",
Expand Down Expand Up @@ -476,13 +478,13 @@ def write_cp2k(
input_template = f_template.read()

pseudos_text = ""
for e in self.elements:
pseudos_text += (
f" &KIND {e}\n"
f" BASIS_SET {basis_set_dict[e]}\n"
f" POTENTIAL {potential_dict[e]}\n"
" &END\n"
)
# for e in self.elements:
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# pseudos_text += (
# f" &KIND {e}\n"
# f" BASIS_SET {basis_set_dict[e]}\n"
# f" POTENTIAL {potential_dict[e]}\n"
# " &END\n"
# )

n_config = self._min_n_config(n_config)
file_id_template = "n_{i}"
Expand Down Expand Up @@ -528,14 +530,16 @@ def write_cp2k(
input_template.format(
file_id=file_id,
structure_name=structure_name,
basis_set=basis_set_directory,
potential=potential_directory,
pseudos_text=pseudos_text,
#basis_set=basis_set_directory,
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#potential=potential_directory,
#pseudos_text=pseudos_text,
cell_x=cell_x,
cell_y=cell_y,
cell_z=cell_z,
cutoff=cutoff,
relcutoff=relcutoff,
param_file_path=param_file_path,
param_file_name=param_file_name,
#cutoff=cutoff,
#relcutoff=relcutoff,
file_xyz=file_xyz_i,
)
)
Expand Down Expand Up @@ -1198,6 +1202,7 @@ def write_n2p2_data(
)

text = ""
lattice_list = [0.,0.,0.,0.,0.,0.,0.,0.,0.]
if n2p2_units is None:
n2p2_units = {"length": "Bohr", "energy": "Ha", "force": "Ha / Bohr"}
n = self._min_n_config(n_config)
Expand All @@ -1206,66 +1211,84 @@ def write_n2p2_data(
xyz_lines = f.readlines()
n_atoms = int(xyz_lines[0].strip())
header_list = xyz_lines[1].split('"')
lattice_list = header_list[1].split()
if n2p2_units["length"] != "Ang":
for j, lattice in enumerate(lattice_list):
lattice_list[j] = float(lattice) / UNITS[n2p2_units["length"]]

if len(header_list) > 1:
lattice_list = header_list[1].split()
if n2p2_units["length"] != "Ang":
for j, lattice in enumerate(lattice_list):
lattice_list[j] = float(lattice) / UNITS[n2p2_units["length"]]
n_structures = int(len(xyz_lines)/ (n_atoms+ 2))
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Very minor but formatting is slightly inconsistent here.

We could also consider assertions to check values that we've inferred are valid e.g. n_atoms

print(n_structures)
with open(join_paths(self.main_directory, file_cp2k_forces.format(i))) as f:
force_lines = f.readlines()

with open(join_paths(self.main_directory, file_cp2k_out.format(i))) as f:
energy = None
energy = []
total_charge = []
charge_lines = []
lines = f.readlines()
for j, line in enumerate(lines):
if re.search("^ ENERGY", line):
energy = line.split()[-1]
energy.append(float(line.split()[-1]))
if re.search("Hirshfeld Charges", line):
charge_lines = lines[j + 3 : j + 3 + n_atoms]
total_charge = lines[j + 3 + n_atoms + 1].split()[-1]

if energy is None:
charge_lines.append(lines[j + 3 : j + 3 + n_atoms])
total_charge.append(float(lines[j + 3 + n_atoms + 1].split()[-1]))
elif re.search("Net charge", line):
charge_lines.append(lines[j + 1 : j + 1 + n_atoms])
total_charge.append(float(lines[j + 1 + n_atoms ].split()[-1]))
if len(header_list) <= 1:
if "Cell lengths [ang]" in line:
print(line.split()[-3],line.split()[-2],line.split()[-1])
lattice_list = [float(line.split()[-3])/ UNITS[n2p2_units["length"]],0.,0.,0., float(line.split()[-2])/ UNITS[n2p2_units["length"]],0.,0.,0., float(line.split()[-1])/ UNITS[n2p2_units["length"]]]
if len(total_charge) == 0:
total_charge = np.zeros_like(energy)
if len(energy) == 0:
raise ValueError("Energy not found in {}".format(file_cp2k_out))
if n2p2_units["energy"] != "Ha":
# cp2k output is in Ha
energy = float(energy) * UNITS["Ha"] / UNITS[n2p2_units["energy"]]

text += "begin\n"
text += "comment config_index={0} units={1}\n".format(i, n2p2_units)
text += "comment structure {}\n".format(structure_name)
text += "lattice {0} {1} {2}\n".format(
lattice_list[0], lattice_list[1], lattice_list[2]
)
text += "lattice {0} {1} {2}\n".format(
lattice_list[3], lattice_list[4], lattice_list[5]
)
text += "lattice {0} {1} {2}\n".format(
lattice_list[6], lattice_list[7], lattice_list[8]
)
for j in range(n_atoms):
atom_xyz = xyz_lines[j + 2].split()
for k, position in enumerate(atom_xyz[1:], 1):
atom_xyz[k] = float(position) / UNITS[n2p2_units["length"]]

force = force_lines[j + 4].split()[-3:]
if n2p2_units["force"] != "Ha / Bohr":
# cp2k output is in Ha / Bohr
for i in range(len(force)):
force[i] = (
float(force[i])
* UNITS["Ha"]
/ UNITS["Bohr"]
/ UNITS[n2p2_units["energy"]]
)

charge = charge_lines[j].split()[-1]
text += "atom {1} {2} {3} {0} {4} 0.0 {5} {6} {7}\n".format(
*atom_xyz + [charge] + force
energy = np.array(energy) * UNITS["Ha"] / UNITS[n2p2_units["energy"]]
for nstr in range(n_structures):
text += "begin\n"
text += "comment config_index={0} units={1}\n".format(i, n2p2_units)
text += "comment structure {}\n".format(structure_name)
text += "lattice {0} {1} {2}\n".format(
lattice_list[-1], lattice_list[1], lattice_list[2]
)
text += "lattice {0} {1} {2}\n".format(
lattice_list[3], lattice_list[4], lattice_list[5]
)
text += "lattice {0} {1} {2}\n".format(
lattice_list[6], lattice_list[7], lattice_list[8]
)
for j in range(nstr*(n_atoms+2), (nstr+1)*(n_atoms + 2) - 2):
atom_xyz = xyz_lines[j + 2].split()[:4]
for k, position in enumerate(atom_xyz[1:], 1):
atom_xyz[k] = float(position) / UNITS[n2p2_units["length"]]
if(n_structures<= 1):
force = force_lines[j + 4].split()[-4:]
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Should be force = force_lines[j + 4].split()[-3:] here and in the else?

else:
force = force_lines[j + 2].split()[-4:]
if n2p2_units["force"] != "Ha / Bohr":
# cp2k output is in Ha / Bohr
for i in range(len(force)):
force[i] = (
float(force[i])
* UNITS["Ha"]
/ UNITS["Bohr"]
/ UNITS[n2p2_units["energy"]]
)

try:
charge = charge_lines[nstr][j].split()[-1]
except:
charge = "0."
#print(j, len(atom_xyz), len(force))
text += "atom {1} {2} {3} {0} {4} 0.0 {5} {6} {7}\n".format(
*atom_xyz + [charge] + force
)

text += "energy {}\n".format(energy)
text += "charge {}\n".format(total_charge)
text += "end\n"
text += "energy {}\n".format(energy[nstr])
text += "charge {}\n".format(total_charge[nstr])
text += "end\n"

for n2p2_directory in self.n2p2_directories:
if isfile(join_paths(n2p2_directory, file_n2p2_input)):
Expand Down