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Merged
njzjz merged 6 commits into from
Mar 20, 2024
Merged

Make improvements to the format for OpenMX #619

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f4b9398
Change the name of OpenMX format from openmx/out to openmx/md
shigeandtomo Mar 18, 2024
5050ec2
Add error message regarding System.Name.md support format
shigeandtomo Mar 18, 2024
efa9103
Add SCF convergence determination
shigeandtomo Mar 19, 2024
c6603af
Add description
shigeandtomo Mar 19, 2024
42659cf
Apply ruff format
shigeandtomo Mar 19, 2024
f0f694b
Add a test for openmx
shigeandtomo Mar 19, 2024
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25 changes: 22 additions & 3 deletions dpdata/openmx/omx.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@
energy_convert = EnergyConversion("hartree", "eV").value()
force_convert = ForceConversion("hartree/bohr", "eV/angstrom").value()

import warnings
from collections import OrderedDict

### iterout.c from OpenMX soure code: column numbers and physical quantities ###
Expand All @@ -28,6 +29,12 @@
# /* 12: magnetic moment (muB) */
# /* 13,14: angles of spin */

# 15: scf_convergence_flag (optional)
#
# 1. Move the declaration of `scf_convergence_flag` in `DFT.c` to `openmx_common.h`.
# 2. Add `scf_convergence_flag` output to the end of `iterout.c` where `*.md` is written.
# 3. Recompile OpenMX.


def load_atom(lines):
atom_names = []
Expand Down Expand Up @@ -70,9 +77,18 @@ def load_cells(lines):
for index, line in enumerate(lines):
if "Cell_Vectors=" in line:
parts = line.split()
cell.append([float(parts[12]), float(parts[13]), float(parts[14])])
cell.append([float(parts[15]), float(parts[16]), float(parts[17])])
cell.append([float(parts[18]), float(parts[19]), float(parts[20])])
if len(parts) == 21: # MD.Type is NVT_NH
cell.append([float(parts[12]), float(parts[13]), float(parts[14])])
cell.append([float(parts[15]), float(parts[16]), float(parts[17])])
cell.append([float(parts[18]), float(parts[19]), float(parts[20])])
elif len(parts) == 16: # MD.Type is Opt
cell.append([float(parts[7]), float(parts[8]), float(parts[9])])
cell.append([float(parts[10]), float(parts[11]), float(parts[12])])
cell.append([float(parts[13]), float(parts[14]), float(parts[15])])
else:
raise RuntimeError(
"Does the file System.Name.md contain unsupported calculation results?"
)
cells.append(cell)
cell = []
cells = np.array(cells)
Expand Down Expand Up @@ -104,6 +120,9 @@ def load_coords(lines, atom_names, natoms):
parts = line.split()
for_line = [float(parts[1]), float(parts[2]), float(parts[3])]
coord.append(for_line)
# It may be necessary to recompile OpenMX to make scf convergence determination.
if len(parts) == 15 and parts[14] == "0":
warnings.warn("SCF in System.Name.md has not converged!")
if cnt == natoms:
coords.append(coord)
cnt = 0
Expand Down
4 changes: 2 additions & 2 deletions dpdata/plugins/openmx.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,15 +3,15 @@
from dpdata.format import Format


@Format.register("openmx/out")
@Format.register("openmx/md")
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@njzjz njzjz Mar 19, 2024

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This might be good, as the old one has never been released.

class OPENMXFormat(Format):
"""Format for the `OpenMX <https://www.openmx-square.org/>`.

OpenMX (Open source package for Material eXplorer) is a nano-scale material simulation package based on DFT, norm-conserving pseudopotentials, and pseudo-atomic localized basis functions.

Note that two output files, System.Name.dat and System.Name.md, are required.

Use the `openmx/out` keyword argument to supply this format.
Use the `openmx/md` keyword argument to supply this format.
"""

@Format.post("rot_lower_triangular")
Expand Down
2,800 changes: 1,400 additions & 1,400 deletions tests/openmx/Methane.md
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Large diffs are not rendered by default.

68 changes: 68 additions & 0 deletions tests/openmx/Methane2.dat
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@@ -0,0 +1,68 @@
#
# File Name
#

System.CurrrentDirectory ./ # default=./
System.Name Methane2
level.of.stdout 1 # default=1 (1-3)
level.of.fileout 1 # default=1 (0-2)

#
# Definition of Atomic Species
#

Species.Number 2
<Definition.of.Atomic.Species
H H5.0-s2 H_PBE19
C C5.0-s2p2 C_PBE19
Definition.of.Atomic.Species>

#
# Atoms
#

Atoms.Number 5
Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU
<Atoms.SpeciesAndCoordinates
1 C 0.300000 0.000000 0.000000 2.0 2.0
2 H -0.889981 -0.629312 0.000000 0.5 0.5
3 H 0.000000 0.629312 -0.889981 0.5 0.5
4 H 0.000000 0.629312 0.889981 0.5 0.5
5 H 0.889981 -0.629312 0.000000 0.5 0.5
Atoms.SpeciesAndCoordinates>
Atoms.UnitVectors.Unit Ang # Ang|AU
#<Atoms.UnitVectors
# 10.0 0.0 0.0
# 0.0 10.0 0.0
# 0.0 0.0 10.0
#Atoms.UnitVectors>

#
# SCF or Electronic System
#

scf.XcType GGA-PBE # LDA|LSDA-CA|LSDA-PW|GGA-PBE
scf.SpinPolarization off # On|Off|NC
scf.ElectronicTemperature 100.0 # default=300 (K)
scf.energycutoff 200.0 # default=150 (Ry)
scf.maxIter 1 # default=40
scf.EigenvalueSolver cluster # DC|GDC|Cluster|Band
scf.Kgrid 1 1 1 # means n1 x n2 x n3
scf.Mixing.Type rmm-diis # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk
scf.Init.Mixing.Weight 0.30 # default=0.30
scf.Min.Mixing.Weight 0.001 # default=0.001
scf.Max.Mixing.Weight 0.400 # default=0.40
scf.Mixing.History 15 # default=5
scf.Mixing.StartPulay 4 # default=6
scf.criterion 1.0e-8 # default=1.0e-6 (Hartree)

#
# MD or Geometry Optimization
#

MD.Type opt # Nomd|Opt|DIIS|NVE|NVT_VS|NVT_NH
MD.Opt.DIIS.History 7 # default=7
MD.Opt.StartDIIS 5 # default=5
MD.maxIter 5 # default=1
MD.TimeStep 1.0 # default=0.5 (fs)
MD.Opt.criterion 1.0e-4 # default=1.0e-4 (Hartree/bohr)
35 changes: 35 additions & 0 deletions tests/openmx/Methane2.md
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@@ -0,0 +1,35 @@
5
time= 0.000 (fs) Energy= -8.15440 (Hartree) Cell_Vectors= 10.00000 0.00000 0.00000 0.00000 10.00000 0.00000 0.00000 0.00000 10.00000
C 0.30000 0.00000 0.00000 -0.36382 0.22843 -0.00000 0.00000 0.00000 0.00000 0.17513 0.00000 0.00000 0.00000 0
H -0.88998 -0.62931 0.00000 0.04918 0.01544 0.00000 0.00000 0.00000 0.00000 -0.07837 0.00000 0.00000 0.00000 0
H 0.00000 0.62931 -0.88998 0.02120 -0.00206 -0.00338 0.00000 0.00000 0.00000 -0.01532 0.00000 0.00000 0.00000 0
H 0.00000 0.62931 0.88998 0.02120 -0.00206 0.00338 0.00000 0.00000 0.00000 -0.01532 0.00000 0.00000 0.00000 0
H 0.88998 -0.62931 0.00000 0.23151 -0.22432 -0.00000 0.00000 0.00000 0.00000 -0.06612 0.00000 0.00000 0.00000 0
5
time= 1.000 (fs) Energy= -8.22382 (Hartree) Cell_Vectors= 10.00000 0.00000 0.00000 0.00000 10.00000 0.00000 0.00000 0.00000 10.00000
C 0.21037 0.05628 -0.00000 -0.12208 -0.03279 0.00000 0.00000 0.00000 0.00000 0.18366 0.00000 0.00000 0.00000 0
H -0.87786 -0.62551 0.00000 0.03791 0.01857 0.00000 0.00000 0.00000 0.00000 -0.08412 0.00000 0.00000 0.00000 0
H 0.00522 0.62881 -0.89081 0.00960 0.01866 -0.02578 0.00000 0.00000 0.00000 -0.03522 0.00000 0.00000 0.00000 0
H 0.00522 0.62881 0.89081 0.00960 0.01866 0.02578 0.00000 0.00000 0.00000 -0.03522 0.00000 0.00000 0.00000 0
H 0.94702 -0.68458 -0.00000 0.04642 -0.02939 -0.00000 0.00000 0.00000 0.00000 -0.02910 0.00000 0.00000 0.00000 0
5
time= 2.000 (fs) Energy= -8.24265 (Hartree) Cell_Vectors= 10.00000 0.00000 0.00000 0.00000 10.00000 0.00000 0.00000 0.00000 10.00000
C 0.12898 0.03442 0.00000 -0.04237 -0.04096 0.00000 0.00000 0.00000 0.00000 0.18611 0.00000 0.00000 0.00000 0
H -0.85259 -0.61313 0.00000 0.01505 0.00643 0.00000 0.00000 0.00000 0.00000 -0.06398 0.00000 0.00000 0.00000 0
H 0.01162 0.64125 -0.90800 0.00781 0.01155 -0.01439 0.00000 0.00000 0.00000 -0.04343 0.00000 0.00000 0.00000 0
H 0.01162 0.64125 0.90800 0.00781 0.01155 0.01439 0.00000 0.00000 0.00000 -0.04343 0.00000 0.00000 0.00000 0
H 0.97796 -0.70417 -0.00000 0.00515 0.00555 -0.00000 0.00000 0.00000 0.00000 -0.03526 0.00000 0.00000 0.00000 0
5
time= 3.000 (fs) Energy= -8.24626 (Hartree) Cell_Vectors= 10.00000 0.00000 0.00000 0.00000 10.00000 0.00000 0.00000 0.00000 10.00000
C 0.10073 0.00711 0.00000 -0.01636 -0.00597 0.00000 0.00000 0.00000 0.00000 0.18796 0.00000 0.00000 0.00000 0
H -0.84256 -0.60884 0.00000 -0.00199 -0.00521 -0.00000 0.00000 0.00000 0.00000 -0.05693 0.00000 0.00000 0.00000 0
H 0.01683 0.64895 -0.91760 0.00694 0.00262 -0.00333 0.00000 0.00000 0.00000 -0.04635 0.00000 0.00000 0.00000 0
H 0.01683 0.64895 0.91760 0.00694 0.00262 0.00333 0.00000 0.00000 0.00000 -0.04635 0.00000 0.00000 0.00000 0
H 0.98139 -0.70048 -0.00000 0.00184 0.00495 -0.00000 0.00000 0.00000 0.00000 -0.03833 0.00000 0.00000 0.00000 0
5
time= 4.000 (fs) Energy= -8.24682 (Hartree) Cell_Vectors= 10.00000 0.00000 0.00000 0.00000 10.00000 0.00000 0.00000 0.00000 10.00000
C 0.08982 0.00313 0.00000 -0.00704 -0.00134 0.00000 0.00000 0.00000 0.00000 0.19038 0.00000 0.00000 0.00000 0
H -0.84389 -0.61232 0.00000 -0.00554 -0.00705 0.00000 0.00000 0.00000 0.00000 -0.05558 0.00000 0.00000 0.00000 0
H 0.02145 0.65069 -0.91982 0.00591 0.00121 -0.00163 0.00000 0.00000 0.00000 -0.04727 0.00000 0.00000 0.00000 0
H 0.02145 0.65069 0.91982 0.00591 0.00121 0.00163 0.00000 0.00000 0.00000 -0.04727 0.00000 0.00000 0.00000 0
H 0.98262 -0.69717 -0.00000 -0.00051 0.00564 -0.00000 0.00000 0.00000 0.00000 -0.04026 0.00000 0.00000 0.00000 0
4 changes: 2 additions & 2 deletions tests/test_openmx.py
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Expand Up @@ -50,12 +50,12 @@ def test_coord(self):

class TestOPENMXTraj(unittest.TestCase, TestOPENMXTRAJProps):
def setUp(self):
self.system = dpdata.System("openmx/Methane", fmt="openmx/out")
self.system = dpdata.System("openmx/Methane", fmt="openmx/md")


class TestOPENMXLabeledTraj(unittest.TestCase, TestOPENMXTRAJProps):
def setUp(self):
self.system = dpdata.LabeledSystem("openmx/Methane", fmt="openmx/out")
self.system = dpdata.LabeledSystem("openmx/Methane", fmt="openmx/md")


if __name__ == "__main__":
Expand Down
62 changes: 62 additions & 0 deletions tests/test_openmx_check_convergence.py
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import unittest

import numpy as np
from context import dpdata


class TestOPENMXTRAJProps:
def test_atom_names(self):
self.assertEqual(self.system.data["atom_names"], ["C", "H"])

def test_atom_numbs(self):
self.assertEqual(self.system.data["atom_numbs"], [1, 4])

def test_atom_types(self):
for ii in range(0, 1):
self.assertEqual(self.system.data["atom_types"][ii], 0)
for ii in range(1, 5):
self.assertEqual(self.system.data["atom_types"][ii], 1)

def test_cell(self):
ref = 10.0 * np.eye(3)
self.assertEqual(self.system.get_nframes(), 5)
for ff in range(self.system.get_nframes()):
for ii in range(3):
for jj in range(3):
self.assertEqual(self.system["cells"][ff][ii][jj], ref[ii][jj])

def test_coord(self):
with open("openmx/Methane2.md") as md_file:
lines = md_file.readlines()
lines = lines[-5:]
coords = []
for line in lines:
parts = line.split()
for_line = [float(parts[1]), float(parts[2]), float(parts[3])]
coords.append(for_line)
coords = np.array(coords)
celll = 10.0
## Applying PBC ##
for ii in range(5):
for jj in range(3):
if coords[ii][jj] < 0:
coords[ii][jj] += celll
elif coords[ii][jj] >= celll:
coords[ii][jj] -= celll
self.assertAlmostEqual(
self.system["coords"][-1][ii][jj], coords[ii][jj]
)


class TestOPENMXTraj(unittest.TestCase, TestOPENMXTRAJProps):
def setUp(self):
self.system = dpdata.System("openmx/Methane2", fmt="openmx/md")


class TestOPENMXLabeledTraj(unittest.TestCase, TestOPENMXTRAJProps):
def setUp(self):
self.system = dpdata.LabeledSystem("openmx/Methane2", fmt="openmx/md")


if __name__ == "__main__":
unittest.main()