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pxlxingliangpre-commit-ci[bot]njzjz
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fix(abacus): fix bug in read LATTICE_CONSTANT in md (#450)
In ABACUS version >= v3.1.4, the format of file "MD_dump" is different. The lattice constant line is added by the unit "Angstrom" at the end, and the position is the real cartesian coordinate. MD_dump is changed from ``` MDSTEP: 0 LATTICE_CONSTANT: 23.453780000000 LATTICE_VECTORS 1.000000000000 0.000000000000 0.000000000000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 0.000000000000 1.000000000000 VIRIAL (KBAR) 36.689617311102 0.000000000001 -0.000000000000 0.000000000001 36.689617311104 -0.000000000001 -0.000000000000 -0.000000000001 36.689617311147 INDEX LABEL POSITIONS FORCE (eV/Angstrom) 0 Sn 0.000000000000 0.000000000000 0.000000000000 -0.000000000000 0.000000000000 -0.000000000000 1 Sn 0.000000000000 0.250000000000 0.250000000000 -0.000186795145 -0.000453823732 -0.000453823732 ``` to ``` MDSTEP: 0 LATTICE_CONSTANT: 12.411200939060 Angstrom LATTICE_VECTORS 1.000000000000 0.000000000000 0.000000000000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 0.000000000000 1.000000000000 VIRIAL (kbar) 36.689617311101 0.000000000003 -0.000000000000 0.000000000003 36.689617311089 -0.000000000001 -0.000000000000 -0.000000000001 36.689617311135 INDEX LABEL POSITION (Angstrom) FORCE (eV/Angstrom) VELOCITY (Angstrom/fs) 0 Sn 0.000000000000 0.000000000000 0.000000000000 -0.000000000000 -0.000000000001 -0.000000000001 0.001244557166 -0.000346684288 0.000768457739 1 Sn 0.000000000000 3.102800034079 3.102800034079 -0.000186795145 -0.000453823768 -0.000453823768 0.000550996187 -0.000886442775 0.001579501983 ``` --------- Signed-off-by: pxlxingliang <91927439+pxlxingliang@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
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Lines changed: 5454 additions & 68 deletions

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‎dpdata/abacus/md.py‎

Lines changed: 31 additions & 50 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,4 @@
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import os
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import re
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import warnings
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import numpy as np
@@ -68,69 +67,51 @@ def get_coords_from_dump(dumplines, natoms):
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for iline in range(nlines):
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if "MDSTEP" in dumplines[iline]:
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# read in LATTICE_CONSTANT
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celldm = float(dumplines[iline + 1].split(" ")[-1])
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# for abacus version >= v3.1.4, the unit is angstrom, and "ANGSTROM" is added at the end
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# for abacus version < v3.1.4, the unit is bohr
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celldm = float(dumplines[iline + 1].split()[1])
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newversion = True
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if "Angstrom" not in dumplines[iline + 1]:
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celldm *= bohr2ang # transfer unit to ANGSTROM
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newversion = False
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# read in LATTICE_VECTORS
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for ix in range(3):
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cells[iframe, ix] = (
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np.array(
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[
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float(i)
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for i in re.split("\s+", dumplines[iline + 3 + ix])[-3:]
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]
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)
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np.array([float(i) for i in dumplines[iline + 3 + ix].split()[0:3]])
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* celldm
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)
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if calc_stress:
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stresses[iframe, ix] = np.array(
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[
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float(i)
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for i in re.split("\s+", dumplines[iline + 7 + ix])[-3:]
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]
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[float(i) for i in dumplines[iline + 7 + ix].split()[0:3]]
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)
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if calc_stress:
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skipline = 11
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else:
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skipline = 7
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for iat in range(total_natoms):
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if calc_stress:
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coords[iframe, iat] = (
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np.array(
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[
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float(i)
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for i in re.split("\s+", dumplines[iline + 11 + iat])[
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-6:-3
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]
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]
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)
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* celldm
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)
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forces[iframe, iat] = np.array(
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[
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float(i)
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for i in re.split("\s+", dumplines[iline + 11 + iat])[-3:]
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]
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)
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else:
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coords[iframe, iat] = (
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np.array(
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[
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float(i)
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for i in re.split("\s+", dumplines[iline + 7 + iat])[
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-6:-3
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]
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]
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)
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* celldm
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)
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forces[iframe, iat] = np.array(
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[
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float(i)
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for i in re.split("\s+", dumplines[iline + 7 + iat])[-3:]
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]
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)
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# INDEX LABEL POSITION (Angstrom) FORCE (eV/Angstrom) VELOCITY (Angstrom/fs)
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# 0 Sn 0.000000000000 0.000000000000 0.000000000000 -0.000000000000 -0.000000000001 -0.000000000001 0.001244557166 -0.000346684288 0.000768457739
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# 1 Sn 0.000000000000 3.102800034079 3.102800034079 -0.000186795145 -0.000453823768 -0.000453823768 0.000550996187 -0.000886442775 0.001579501983
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# for abacus version >= v3.1.4, the value of POSITION is the real cartessian position, and unit is angstrom, and if cal_force the VELOCITY is added at the end.
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# for abacus version < v3.1.4, the real position = POSITION * celldm
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coords[iframe, iat] = np.array(
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[float(i) for i in dumplines[iline + skipline + iat].split()[2:5]]
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)
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if not newversion:
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coords[iframe, iat] *= celldm
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forces[iframe, iat] = np.array(
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[float(i) for i in dumplines[iline + skipline + iat].split()[5:8]]
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)
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iframe += 1
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assert iframe == nframes_dump, (
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"iframe=%d, nframe_dump=%d. Number of frames does not match number of lines in MD_dump."
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% (iframe, nframes_dump)
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)
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cells *= bohr2ang
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coords *= bohr2ang
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stresses *= kbar2evperang3
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return coords, cells, forces, stresses
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‎tests/abacus.md.newversion/INPUT‎

Lines changed: 37 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,37 @@
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INPUT_PARAMETERS
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#Parameters (1.General)
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suffix Sn_nve
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calculation md
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ntype 1
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nbands 160
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symmetry 0
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pseudo_dir ../../../tests/PP_ORB
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orbital_dir ../../../tests/PP_ORB
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#Parameters (2.Iteration)
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ecutwfc 30
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scf_thr 1e-5
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scf_nmax 100
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#Parameters (3.Basis)
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basis_type lcao
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ks_solver genelpa
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gamma_only 1
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#Parameters (4.Smearing)
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smearing_method gaussian
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smearing_sigma 0.01
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#Parameters (5.Mixing)
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mixing_type pulay
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mixing_beta 0.3
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chg_extrap second-order
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30+
#Parameters (6.MD)
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md_type 0
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md_nstep 10
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md_dt 1
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md_tfirst 300
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cal_force 1
37+
cal_stress 1

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