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fix(abacus): do not write to deepmd raw/npy, if no abacus data in post_fp_abacus_scf() #1153

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merged 5 commits into from
Mar 19, 2023
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fix(abacus): do not write to deepmd raw/npy, if no abacus data in post_fp_abacus_scf() #1153

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cdb57fd
fix(abacus): do not write to deepmd raw/npy, if no abacus data in pos…
pxlxingliang Mar 16, 2023
be6e5dd
Merge branch 'devel' of github.com:deepmodeling/dpgen into abacusrun
pxlxingliang Mar 17, 2023
a536c35
add the unittest with failed job
pxlxingliang Mar 17, 2023
ea2df4c
add running_scf.log file
pxlxingliang Mar 17, 2023
9c95e7b
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 17, 2023
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26 changes: 10 additions & 16 deletions dpgen/generator/run.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4061,27 +4061,21 @@ def post_fp_abacus_scf(iter_index, jdata):
sys_output.sort()
sys_input.sort()

flag = True
all_sys = None
for ii, oo in zip(sys_input, sys_output):
if flag:
_sys = dpdata.LabeledSystem(
oo, fmt="abacus/scf", type_map=jdata["type_map"]
)
if len(_sys) > 0:
_sys = dpdata.LabeledSystem(
oo, fmt="abacus/scf", type_map=jdata["type_map"]
)
if len(_sys) > 0:
if all_sys == None:
all_sys = _sys
flag = False
else:
pass
else:
_sys = dpdata.LabeledSystem(
oo, fmt="abacus/scf", type_map=jdata["type_map"]
)
if len(_sys) > 0:
all_sys.append(_sys)

sys_data_path = os.path.join(work_path, "data.%s" % ss)
all_sys.to_deepmd_raw(sys_data_path)
all_sys.to_deepmd_npy(sys_data_path, set_size=len(sys_output))
if all_sys != None:
sys_data_path = os.path.join(work_path, "data.%s" % ss)
all_sys.to_deepmd_raw(sys_data_path)
all_sys.to_deepmd_npy(sys_data_path, set_size=len(sys_output))


def post_fp_siesta(iter_index, jdata):
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14 changes: 14 additions & 0 deletions tests/generator/out_data_post_fp_abacus/02.fp/task.001.000002/INPUT
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INPUT_PARAMETERS
ntype 2
pseudo_dir ./
ecutwfc 80.000000
mixing_type pulay
mixing_beta 0.400000
symmetry 1
nbands 5.000000
nspin 1
ks_solver cg
smearing fixed
sigma 0.001000
force 1
stress 1
4 changes: 4 additions & 0 deletions tests/generator/out_data_post_fp_abacus/02.fp/task.001.000002/KPT
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K_POINTS
0
Gamma
1 1 1 0 0 0
198 changes: 198 additions & 0 deletions tests/generator/out_data_post_fp_abacus/02.fp/task.001.000002/OUT.ABACUS/running_scf.log
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ABACUS v3.1

Atomic-orbital Based Ab-initio Computation at UStc

Website: http://abacus.ustc.edu.cn/
Documentation: https://abacus.deepmodeling.com/
Repository: https://github.com/abacusmodeling/abacus-develop
https://github.com/deepmodeling/abacus-develop

Start Time is Wed Mar 15 18:24:30 2023

------------------------------------------------------------------------------------

READING GENERAL INFORMATION
global_out_dir = OUT.ABACUS/
global_in_card = INPUT
pseudo_dir =
orbital_dir =
DRANK = 1
DSIZE = 8
DCOLOR = 1
GRANK = 1
GSIZE = 1
The esolver type has been set to : ksdft_lcao




>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
| |
| Reading atom information in unitcell: |
| From the input file and the structure file we know the number of |
| different elments in this unitcell, then we list the detail |
| information for each element, especially the zeta and polar atomic |
| orbital number for each element. The total atom number is counted. |
| We calculate the nearest atom distance for each atom and show the |
| Cartesian and Direct coordinates for each atom. We list the file |
| address for atomic orbitals. The volume and the lattice vectors |
| in real and reciprocal space is also shown. |
| |
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<




READING UNITCELL INFORMATION
ntype = 2
atom label for species 1 = H
atom label for species 2 = O
lattice constant (Bohr) = 1.88973
lattice constant (Angstrom) = 1

READING ATOM TYPE 1
atom label = H
L=0, number of zeta = 2
L=1, number of zeta = 1
number of atom for this type = 2
start magnetization = FALSE
start magnetization = FALSE

READING ATOM TYPE 2
atom label = O
L=0, number of zeta = 2
L=1, number of zeta = 2
L=2, number of zeta = 1
number of atom for this type = 1
start magnetization = FALSE

TOTAL ATOM NUMBER = 3

CARTESIAN COORDINATES ( UNIT = 1.88973 Bohr ).
atom x y z mag vx vy vz
tauc_H1 10.1236 0.358121000009 2.96728000001 0 0 0 0
tauc_H2 10.097 0.457652000002 1.52015 0 0 0 0
tauc_O1 10.263 0.407492999997 3.07706999999 0 0 0 0


READING ORBITAL FILE NAMES FOR LCAO
orbital file: H_gga_6au_60Ry_2s1p.orb
orbital file: O_gga_6au_60Ry_2s2p1d.orb

Volume (Bohr^3) = 22712.4312372
Volume (A^3) = 3365.6310456

Lattice vectors: (Cartesian coordinate: in unit of a_0)
+14.9758141613 +0 +0
-0.1998739632 +14.9158454229 +0
+0.0479160432 +0.2573204003 +15.0670665885
Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0)
+0.066774332883 +0.000894783378008 -0.00022763607076
-0 +0.0670427972165 -0.00114497930408
+0 -0 +0.066369919727




>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
| |
| Reading pseudopotentials files: |
| The pseudopotential file is in UPF format. The 'NC' indicates that |
| the type of pseudopotential is 'norm conserving'. Functional of |
| exchange and correlation is decided by 4 given parameters in UPF |
| file. We also read in the 'core correction' if there exists. |
| Also we can read the valence electrons number and the maximal |
| angular momentum used in this pseudopotential. We also read in the |
| trail wave function, trail atomic density and local-pseudopotential|
| on logrithmic grid. The non-local pseudopotential projector is also|
| read in if there is any. |
| |
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<




PAO radial cut off (Bohr) = 15

Read in pseudopotential file is H_ONCV_PBE-1.0.upf
pseudopotential type = NC
exchange-correlation functional = PBE
nonlocal core correction = 0
valence electrons = 1
lmax = 0
number of zeta = 0
number of projectors = 2
L of projector = 0
L of projector = 0

In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file
Please make sure this is what you need
XC functional updated to : lda
exchange-correlation functional = LDA
PAO radial cut off (Bohr) = 15

Read in pseudopotential file is O_ONCV_PBE-1.0.upf
pseudopotential type = NC
exchange-correlation functional = PBE
nonlocal core correction = 0
valence electrons = 6
lmax = 1
number of zeta = 0
number of projectors = 4
L of projector = 0
L of projector = 0
L of projector = 1
L of projector = 1

In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file
Please make sure this is what you need
XC functional updated to : lda
exchange-correlation functional = LDA

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%% WARNING WARNING WARNING WARNING WARNING %%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
!!! WARNING: Some atoms are too close!!!
!!! Please check the nearest-neighbor list in log file.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%% WARNING WARNING WARNING WARNING WARNING %%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%% WARNING WARNING WARNING WARNING WARNING %%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
!!! WARNING: Some atoms are too close!!!
!!! Please check the nearest-neighbor list in log file.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%% WARNING WARNING WARNING WARNING WARNING %%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%% WARNING WARNING WARNING WARNING WARNING %%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
!!! WARNING: Some atoms are too close!!!
!!! Please check the nearest-neighbor list in log file.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%% WARNING WARNING WARNING WARNING WARNING %%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1-th H, 1-th O (cell: 0 0 0), distance= 0.348 Bohr (0.184 Angstrom)
If this structure is what you want, you can set 'min_dist_coef'
as a smaller value (the current value is 0.2) in INPUT file.
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
NOTICE
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

The structure is unreasonable!
CHECK IN FILE : OUT.ABACUS/warning.log

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
NOTICE
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Check in file : OUT.ABACUS/warning.log




|CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%-------
----------------------------------------------------------------------------------------
13 changes: 13 additions & 0 deletions tests/generator/out_data_post_fp_abacus/02.fp/task.001.000002/POSCAR
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H4 C1
1.0
1.0256560185400000e+01 0.0000000000000000e+00 0.0000000000000000e+00
-2.4531774970000000e-01 9.8128484190999998e+00 0.0000000000000000e+00
-2.5710315189999999e-01 -3.0129123369999999e-01 9.8293471193999995e+00
H C
4 1
Cartesian
5.3475200000 4.1329900000 3.4240900000
4.0099600000 5.0100700000 4.1737100000
5.5891800000 5.0824200000 4.8661200000
4.7052500000 3.5190100000 4.8860700000
4.9222700000 4.4726500000 4.3767300000
25 changes: 25 additions & 0 deletions tests/generator/out_data_post_fp_abacus/02.fp/task.001.000002/STRU
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ATOMIC_SPECIES
H 1.00 H_ONCV_PBE-1.0.upf
C 1.00 C_ONCV_PBE-1.0.upf

LATTICE_CONSTANT
1.8897261254578281

LATTICE_VECTORS
10.2565601854 0.0 0.0
-0.2453177497 9.8128484191 0.0
-0.2571031519 -0.3012912337 9.8293471194

ATOMIC_POSITIONS
Cartesian # Cartesian(Unit is LATTICE_CONSTANT)
H
0.0
4
5.347520000000 4.132990000000 3.424090000000 0 0 0
4.009960000000 5.010070000000 4.173710000000 0 0 0
5.589180000000 5.082420000000 4.866120000000 0 0 0
4.705250000000 3.519010000000 4.886070000000 0 0 0
C
0.0
1
4.922270000000 4.472650000000 4.376730000000 0 0 0
67 changes: 67 additions & 0 deletions tests/generator/out_data_post_fp_abacus/02.fp/task.001.000002/output
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WARNING: Total thread number on this node mismatches with hardware availability. This may cause poor performance.
Info: Local MPI proc number: 8,OpenMP thread number: 1,Total thread number: 8,Local thread limit: 16

ABACUS v3.1

Atomic-orbital Based Ab-initio Computation at UStc

Website: http://abacus.ustc.edu.cn/
Documentation: https://abacus.deepmodeling.com/
Repository: https://github.com/abacusmodeling/abacus-develop
https://github.com/deepmodeling/abacus-develop

Wed Mar 15 18:24:30 2023
MAKE THE DIR : OUT.ABACUS/
dft_functional readin is: lda
dft_functional in pseudopot file is: PBE
In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file
Please make sure this is what you need
dft_functional readin is: lda
dft_functional in pseudopot file is: PBE
In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file
Please make sure this is what you need

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%% WARNING WARNING WARNING WARNING WARNING %%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
!!! WARNING: Some atoms are too close!!!
!!! Please check the nearest-neighbor list in log file.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%% WARNING WARNING WARNING WARNING WARNING %%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%% WARNING WARNING WARNING WARNING WARNING %%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
!!! WARNING: Some atoms are too close!!!
!!! Please check the nearest-neighbor list in log file.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%% WARNING WARNING WARNING WARNING WARNING %%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%% WARNING WARNING WARNING WARNING WARNING %%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
!!! WARNING: Some atoms are too close!!!
!!! Please check the nearest-neighbor list in log file.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%% WARNING WARNING WARNING WARNING WARNING %%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

If this structure is what you want, you can set 'min_dist_coef'
as a smaller value (the current value is 0.2) in INPUT file.

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
NOTICE
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

The structure is unreasonable!
CHECK IN FILE : OUT.ABACUS/warning.log

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
NOTICE
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

|CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%-------
----------------------------------------------------------------------------------------
See output information in : OUT.ABACUS/
3 changes: 3 additions & 0 deletions tests/generator/test_post_fp.py
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Expand Up @@ -223,6 +223,9 @@ def setUp(self):
"iter.000000/02.fp/data.000", fmt="deepmd/raw"
)

def test_nframs_with_failed_job(self):
self.assertEqual(self.system_2.get_nframes(), 2)


class TestPostFPSIESTA(unittest.TestCase, CompLabeledSys):
def setUp(self):
Expand Down