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Merged
jacobfilik merged 1 commit into from
Jun 23, 2025
Merged

Use cell parameters for qe cell geometry #19

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35 changes: 26 additions & 9 deletions web-conexs-api/src/web_conexs_api/jobfilebuilders.py
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
import math
import io
import re

import numpy as np
from pymatgen.core import Molecule
from pymatgen.core import Lattice, Molecule

from .models.models import (
ConductivityType,
Expand Down Expand Up @@ -86,7 +86,7 @@ def build_orca_input_file(
jobfile += " OPT "

if orca_simulation.solvent is not None:
jobfile += "CPCM(" + orca_simulation.solvent + ") "
jobfile += " CPCM(" + orca_simulation.solvent.value + ") "

jobfile += "\n"

Expand Down Expand Up @@ -158,6 +158,17 @@ def build_qe_inputfile(qe_simulation: QESimulation, structure: CrystalStructure)

n_type = len(element_set) + 1

lattice = Lattice.from_parameters(
a=structure.a,
b=structure.b,
c=structure.c,
alpha=structure.alpha,
beta=structure.beta,
gamma=structure.gamma,
)

matrix = lattice.matrix

jobfile = "&CONTROL \n"
jobfile += " calculation = 'scf'\n"
jobfile += " etot_conv_thr = 1.0000000000d-05\n"
Expand All @@ -172,12 +183,7 @@ def build_qe_inputfile(qe_simulation: QESimulation, structure: CrystalStructure)
jobfile += "/ \n\n"

jobfile += "&SYSTEM \n"
jobfile += " A = " + str(structure.a) + "\n"
jobfile += " B = " + str(structure.b) + "\n"
jobfile += " C = " + str(structure.c) + "\n"
jobfile += " cosBC = " + str(math.cos(math.radians(structure.alpha))) + "\n"
jobfile += " cosAC = " + str(math.cos(math.radians(structure.beta))) + "\n"
jobfile += " cosAB = " + str(math.cos(math.radians(structure.gamma))) + "\n"
jobfile += " ibrav = 0\n"

if qe_simulation.conductivity == ConductivityType.metallic:
occupations = "smearing"
Expand Down Expand Up @@ -251,6 +257,17 @@ def build_qe_inputfile(qe_simulation: QESimulation, structure: CrystalStructure)
jobfile += "1 1 1 0 0 0\n"
jobfile += "\n\n"

jobfile += "CELL_PARAMETERS {angstrom}\n"

print(np.array2string(matrix))
s = io.BytesIO()

np.savetxt(s, matrix)

jobfile += s.getvalue().decode()

jobfile += "\n"

return (
jobfile,
qe_simulation.absorbing_atom,
Expand Down
11 changes: 8 additions & 3 deletions web-conexs-api/tests/test_jobfile_builder.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@
MolecularStructure,
OrcaCalculation,
OrcaSimulation,
OrcaSolvent,
QEEdge,
QESimulation,
Simulation,
Expand All @@ -37,10 +38,14 @@ def test_orca_xas_filebuilder():

jobfile = build_orca_input_file(test_model, test_structure)

print(jobfile)

assert "%tddft" in jobfile

test_model.solvent = OrcaSolvent.Water

jobfile = build_orca_input_file(test_model, test_structure)

assert "CPCM(Water)" in jobfile


def test_orca_opt_filebuilder():
test_simulation = Simulation(n_cores=1)
Expand Down Expand Up @@ -89,7 +94,7 @@ def test_qe_filebuilder():
test_model, test_structure
)

assert "cosAB" in jobfile
assert "CELL_PARAMETERS" in jobfile


def test_fdmnes_crystal_filebuilder():
Expand Down