QE: Support output files without stress (#572)

Yi-FanLi · pre-commit-ci[bot] · web-flow · commit e52b6992bf54 · 2023-11-06T11:34:22.000+08:00
support qe output files which do not contain stress

---------

Co-authored-by: pre-commit-ci[bot] &lt;66853113+pre-commit-ci[bot]@users.noreply.github.com&gt;
diff --git a/dpdata/plugins/qe.py b/dpdata/plugins/qe.py
@@ -46,6 +46,8 @@ def from_labeled_system(self, file_name, **kwargs):
             data["coords"],
             data["energies"],
             data["forces"],
-            data["virials"],
+            tmp_virial,
         ) = dpdata.qe.scf.get_frame(file_name)
+        if tmp_virial is not None:
+            data["virials"] = tmp_virial
         return data
diff --git a/dpdata/qe/scf.py b/dpdata/qe/scf.py
@@ -120,6 +120,8 @@ def get_force(lines, natoms):
 
 def get_stress(lines):
     blk = get_block(lines, "total   stress")
+    if len(blk) == 0:
+        return
     ret = []
     for ii in blk:
         ret.append([float(jj) for jj in ii.split()[3:6]])
@@ -148,7 +150,9 @@ def get_frame(fname):
     atom_names, natoms, types, coords = get_coords(inlines, cell)
     energy = get_energy(outlines)
     force = get_force(outlines, natoms)
-    stress = get_stress(outlines) * np.linalg.det(cell)
+    stress = get_stress(outlines)
+    if stress is not None:
+        stress = (stress * np.linalg.det(cell))[np.newaxis, :, :]
     return (
         atom_names,
         natoms,
@@ -157,5 +161,5 @@ def get_frame(fname):
         coords[np.newaxis, :, :],
         np.array(energy)[np.newaxis],
         force[np.newaxis, :, :],
-        stress[np.newaxis, :, :],
+        stress,
     )
diff --git a/tests/qe.scf/03.in b/tests/qe.scf/03.in
@@ -0,0 +1,37 @@
+&control
+  calculation='scf'
+  prefix='water'
+  pseudo_dir='../pseudo'
+  outdir='./out'
+  restart_mode='from_scratch'
+  nstep=20000
+  disk_io='none'
+  max_seconds=10000
+  tprnfor=.true.
+  tstress=.false.
+/
+&system
+  ibrav=1
+  a=10
+  nat=5
+  ntyp=2,
+  ecutwfc=110
+  input_dft='PBE'
+/
+&electrons
+  electron_maxstep = 1000
+  mixing_beta = 0.5
+/
+&ions
+/
+&cell
+/
+ATOMIC_SPECIES
+H   1.0  H.pbe-van_ak.UPF
+C   1.0  C.pbe-van_ak.UPF 
+ATOMIC_POSITIONS {angstrom}
+H 5.41646 4.01132 3.51118
+H 4.13161 4.70677 4.43116
+H 5.63096 5.52167 4.45038
+H 5.49988 4.00341 5.34265
+C 5.19271 4.55775 4.43687
diff --git a/tests/qe.scf/03.out b/tests/qe.scf/03.out
@@ -0,0 +1,314 @@
+
+     Program PWSCF v.7.1 starts on  5Nov2023 at 13:51:57 
+
+     This program is part of the open-source Quantum ESPRESSO suite
+     for quantum simulation of materials; please cite
+         "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
+         "P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);
+         "P. Giannozzi et al., J. Chem. Phys. 152 154105 (2020);
+          URL http://www.quantum-espresso.org", 
+     in publications or presentations arising from this work. More details at
+     http://www.quantum-espresso.org/quote
+
+     Parallel version (MPI), running on    28 processors
+
+     MPI processes distributed on     1 nodes
+     59927 MiB available memory on the printing compute node when the environment starts
+ 
+     Waiting for input...
+     Reading input from standard input
+Warning: card &CELL ignored
+Warning: card / ignored
+
+     Current dimensions of program PWSCF are:
+     Max number of different atomic species (ntypx) = 10
+     Max number of k-points (npk) =  40000
+     Max angular momentum in pseudopotentials (lmaxx) =  4
+
+     IMPORTANT: XC functional enforced from input :
+     Exchange-correlation= PBE
+                           (   1   4   3   4   0   0   0)
+     Any further DFT definition will be discarded
+     Please, verify this is what you really want
+
+
+     gamma-point specific algorithms are used
+ 
+     R & G space division:  proc/nbgrp/npool/nimage =      28
+     Subspace diagonalization in iterative solution of the eigenvalue problem:
+     a serial algorithm will be used
+
+ 
+     Parallelization info
+     --------------------
+     sticks:   dense  smooth     PW     G-vecs:    dense   smooth      PW
+     Min         446     446    110                37558    37558    4694
+     Max         448     448    112                37564    37564    4708
+     Sum       12517   12517   3125              1051747  1051747  131683
+ 
+     Using Slab Decomposition
+ 
+
+
+     bravais-lattice index     =            1
+     lattice parameter (alat)  =      18.8973  a.u.
+     unit-cell volume          =    6748.3345 (a.u.)^3
+     number of atoms/cell      =            5
+     number of atomic types    =            2
+     number of electrons       =         8.00
+     number of Kohn-Sham states=            4
+     kinetic-energy cutoff     =     110.0000  Ry
+     charge density cutoff     =     440.0000  Ry
+     scf convergence threshold =      1.0E-06
+     mixing beta               =       0.5000
+     number of iterations used =            8  plain     mixing
+     Exchange-correlation= PBE
+                           (   1   4   3   4   0   0   0)
+
+     celldm(1)=  18.897261  celldm(2)=   0.000000  celldm(3)=   0.000000
+     celldm(4)=   0.000000  celldm(5)=   0.000000  celldm(6)=   0.000000
+
+     crystal axes: (cart. coord. in units of alat)
+               a(1) = (   1.000000   0.000000   0.000000 )  
+               a(2) = (   0.000000   1.000000   0.000000 )  
+               a(3) = (   0.000000   0.000000   1.000000 )  
+
+     reciprocal axes: (cart. coord. in units 2 pi/alat)
+               b(1) = (  1.000000  0.000000  0.000000 )  
+               b(2) = (  0.000000  1.000000  0.000000 )  
+               b(3) = (  0.000000  0.000000  1.000000 )  
+
+
+     PseudoPot. # 1 for H  read from file:
+     ../pseudo/H.pbe-van_ak.UPF
+     MD5 check sum: a537b41238c433fb4068aaff04c6fb4a
+     Pseudo is Ultrasoft, Zval =  1.0
+     Generated by new atomic code, or converted to UPF format
+     Using radial grid of  615 points,  1 beta functions with: 
+                l(1) =   0
+     Q(r) pseudized with  8 coefficients,  rinner =    0.800
+
+     PseudoPot. # 2 for C  read from file:
+     ../pseudo/C.pbe-van_ak.UPF
+     MD5 check sum: ecc3b1e1c1ebe006fc976faab44e17a8
+     Pseudo is Ultrasoft, Zval =  4.0
+     Generated by new atomic code, or converted to UPF format
+     Using radial grid of  721 points,  4 beta functions with: 
+                l(1) =   0
+                l(2) =   0
+                l(3) =   1
+                l(4) =   1
+     Q(r) pseudized with  8 coefficients,  rinner =    0.800   0.800   0.800
+
+
+     atomic species   valence    mass     pseudopotential
+        H              1.00     1.00000     H ( 1.00)
+        C              4.00     1.00000     C ( 1.00)
+
+     No symmetry found
+
+
+
+   Cartesian axes
+
+     site n.     atom                  positions (alat units)
+         1           H   tau(   1) = (   0.5416460   0.4011320   0.3511180  )
+         2           H   tau(   2) = (   0.4131610   0.4706770   0.4431160  )
+         3           H   tau(   3) = (   0.5630960   0.5521670   0.4450380  )
+         4           H   tau(   4) = (   0.5499880   0.4003410   0.5342650  )
+         5           C   tau(   5) = (   0.5192710   0.4557750   0.4436870  )
+
+     number of k points=     1
+                       cart. coord. in units 2pi/alat
+        k(    1) = (   0.0000000   0.0000000   0.0000000), wk =   2.0000000
+
+     Dense  grid:   525874 G-vectors     FFT dimensions: ( 128, 128, 128)
+
+     Estimated max dynamical RAM per process >      30.88 MB
+
+     Estimated total dynamical RAM >     864.60 MB
+
+     Initial potential from superposition of free atoms
+
+     starting charge       7.9999, renormalised to       8.0000
+
+     negative rho (up, down):  1.567E-03 0.000E+00
+     Starting wfcs are    8 randomized atomic wfcs
+
+     total cpu time spent up to now is        0.7 secs
+
+     Self-consistent Calculation
+
+     iteration #  1     ecut=   110.00 Ry     beta= 0.50
+     Davidson diagonalization with overlap
+     ethr =  1.00E-02,  avg # of iterations =  2.0
+
+     negative rho (up, down):  3.779E-03 0.000E+00
+
+     total cpu time spent up to now is        0.9 secs
+
+     total energy              =     -16.02157560 Ry
+     estimated scf accuracy    <       0.70040947 Ry
+
+     iteration #  2     ecut=   110.00 Ry     beta= 0.50
+     Davidson diagonalization with overlap
+     ethr =  8.76E-03,  avg # of iterations =  2.0
+
+     negative rho (up, down):  4.476E-03 0.000E+00
+
+     total cpu time spent up to now is        1.1 secs
+
+     total energy              =     -16.15192549 Ry
+     estimated scf accuracy    <       0.04051988 Ry
+
+     iteration #  3     ecut=   110.00 Ry     beta= 0.50
+     Davidson diagonalization with overlap
+     ethr =  5.06E-04,  avg # of iterations =  1.0
+
+     negative rho (up, down):  5.628E-03 0.000E+00
+
+     total cpu time spent up to now is        1.2 secs
+
+     total energy              =     -16.14738168 Ry
+     estimated scf accuracy    <       0.01107922 Ry
+
+     iteration #  4     ecut=   110.00 Ry     beta= 0.50
+     Davidson diagonalization with overlap
+     ethr =  1.38E-04,  avg # of iterations =  2.0
+
+     negative rho (up, down):  5.562E-03 0.000E+00
+
+     total cpu time spent up to now is        1.4 secs
+
+     total energy              =     -16.14875721 Ry
+     estimated scf accuracy    <       0.00199039 Ry
+
+     iteration #  5     ecut=   110.00 Ry     beta= 0.50
+     Davidson diagonalization with overlap
+     ethr =  2.49E-05,  avg # of iterations =  2.0
+
+     negative rho (up, down):  5.643E-03 0.000E+00
+
+     total cpu time spent up to now is        1.5 secs
+
+     total energy              =     -16.14865735 Ry
+     estimated scf accuracy    <       0.00032165 Ry
+
+     iteration #  6     ecut=   110.00 Ry     beta= 0.50
+     Davidson diagonalization with overlap
+     ethr =  4.02E-06,  avg # of iterations =  3.0
+
+     negative rho (up, down):  5.623E-03 0.000E+00
+
+     total cpu time spent up to now is        1.7 secs
+
+     total energy              =     -16.14878943 Ry
+     estimated scf accuracy    <       0.00003385 Ry
+
+     iteration #  7     ecut=   110.00 Ry     beta= 0.50
+     Davidson diagonalization with overlap
+     ethr =  4.23E-07,  avg # of iterations =  2.0
+
+     negative rho (up, down):  5.612E-03 0.000E+00
+
+     total cpu time spent up to now is        1.9 secs
+
+     total energy              =     -16.14877906 Ry
+     estimated scf accuracy    <       0.00003129 Ry
+
+     iteration #  8     ecut=   110.00 Ry     beta= 0.50
+     Davidson diagonalization with overlap
+     ethr =  3.91E-07,  avg # of iterations =  2.0
+
+     negative rho (up, down):  5.611E-03 0.000E+00
+
+     total cpu time spent up to now is        2.0 secs
+
+     total energy              =     -16.14878120 Ry
+     estimated scf accuracy    <       0.00000208 Ry
+
+     iteration #  9     ecut=   110.00 Ry     beta= 0.50
+     Davidson diagonalization with overlap
+     ethr =  2.61E-08,  avg # of iterations =  3.0
+
+     negative rho (up, down):  5.614E-03 0.000E+00
+
+     total cpu time spent up to now is        2.2 secs
+
+     End of self-consistent calculation
+
+          k = 0.0000 0.0000 0.0000 ( 65842 PWs)   bands (ev):
+
+   -16.9477  -9.4968  -9.3276  -9.0865
+
+     highest occupied level (ev):    -9.0865
+
+!    total energy              =     -16.14878191 Ry
+     estimated scf accuracy    <       0.00000062 Ry
+
+     The total energy is the sum of the following terms:
+     one-electron contribution =     -40.61130475 Ry
+     hartree contribution      =      21.13447342 Ry
+     xc contribution           =      -6.37239920 Ry
+     ewald contribution        =       9.70044862 Ry
+
+     convergence has been achieved in   9 iterations
+
+     Forces acting on atoms (cartesian axes, Ry/au):
+
+     atom    1 type  1   force =     0.01321833    0.00035039    0.00596821
+     atom    2 type  1   force =    -0.03792494    0.00068257    0.00934494
+     atom    3 type  1   force =     0.03068281    0.04387976   -0.00506668
+     atom    4 type  1   force =    -0.00384202    0.00079975   -0.01397316
+     atom    5 type  2   force =    -0.00213417   -0.04571247    0.00372669
+
+     Total force =     0.083354     Total SCF correction =     0.000416
+ 
+     init_run     :      0.39s CPU      0.59s WALL (       1 calls)
+     electrons    :      1.44s CPU      1.49s WALL (       1 calls)
+     forces       :      0.09s CPU      0.09s WALL (       1 calls)
+
+     Called by init_run:
+     wfcinit      :      0.02s CPU      0.05s WALL (       1 calls)
+     potinit      :      0.09s CPU      0.13s WALL (       1 calls)
+     hinit0       :      0.05s CPU      0.10s WALL (       1 calls)
+
+     Called by electrons:
+     c_bands      :      0.22s CPU      0.24s WALL (       9 calls)
+     sum_band     :      0.30s CPU      0.32s WALL (       9 calls)
+     v_of_rho     :      0.60s CPU      0.65s WALL (      10 calls)
+     newd         :      0.24s CPU      0.29s WALL (      10 calls)
+     mix_rho      :      0.12s CPU      0.12s WALL (       9 calls)
+
+     Called by c_bands:
+     init_us_2    :      0.01s CPU      0.01s WALL (      19 calls)
+     init_us_2:cp :      0.01s CPU      0.01s WALL (      19 calls)
+     regterg      :      0.21s CPU      0.22s WALL (       9 calls)
+
+     Called by *egterg:
+     rdiaghg      :      0.00s CPU      0.02s WALL (      28 calls)
+     h_psi        :      0.20s CPU      0.22s WALL (      29 calls)
+     s_psi        :      0.00s CPU      0.00s WALL (      29 calls)
+     g_psi        :      0.00s CPU      0.00s WALL (      19 calls)
+
+     Called by h_psi:
+     h_psi:calbec :      0.01s CPU      0.02s WALL (      29 calls)
+     vloc_psi     :      0.19s CPU      0.19s WALL (      29 calls)
+     add_vuspsi   :      0.00s CPU      0.01s WALL (      29 calls)
+
+     General routines
+     calbec       :      0.01s CPU      0.02s WALL (      42 calls)
+     fft          :      0.38s CPU      0.45s WALL (      92 calls)
+     ffts         :      0.03s CPU      0.03s WALL (       9 calls)
+     fftw         :      0.17s CPU      0.18s WALL (     128 calls)
+ 
+     Parallel routines
+ 
+     PWSCF        :      1.98s CPU      2.31s WALL
+
+ 
+   This run was terminated on:  13:52: 0   5Nov2023            
+
+=------------------------------------------------------------------------------=
+   JOB DONE.
+=------------------------------------------------------------------------------=
diff --git a/tests/qe.scf/ch4_force_2 b/tests/qe.scf/ch4_force_2
@@ -0,0 +1,5 @@
+3.398569258943536786e-01 9.008889040001466508e-03 1.534488474483494125e-01 
+-9.750894041174495985e-01 1.754958015934758586e-02 2.402680657138368536e-01 
+7.888867568293825849e-01 1.128193980826777798e+00 -1.302695793863826723e-01 
+-9.878230505855312149e-02 2.056239906886946772e-02 -3.592643853368728823e-01 
+-5.487171643739811866e-02 -1.175314849094996283e+00 9.581705156106927468e-02
diff --git a/tests/test_qe_pw_scf.py b/tests/test_qe_pw_scf.py
