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misa...@gmail.com
Sep 9, 2017, 3:03:18 AM9/9/17
to Quantum-Dynamics-Hub
Dear Alexey,
py-scr2.py,
submit_templ.pbs,
Thank you. Looking forward to your reply.
Error in /wd/job0/CRASH,
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% task # 14 from pw_readfile : error # 1 error opening xml data file %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% task # 10 from pw_readfile : error # 1 error opening xml data file %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% task # 13 from pw_readfile : error # 1 error opening xml data file %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
from PYXAID import *import os
nsteps_per_job = 2tot_nsteps = 4
os.system("rm -rf wd")os.system("rm -rf res")os.system("mkdir res")
# Step 1 - split MD trajectory on the time steps# Provide files listed below: "x.md.out" and "x.scf.in"# IMPORTANT: # 1) use only ABSOLUTE path for PP in x.scf.in file# 2) provided input file is just a template, so do not include coordinates#out2inp.out2inp("x.md.out","x0.scf.in","wd","x0.scf",0,tot_nsteps,1) # neutral setup#out2inp.out2inp("x.md.out","x1.scf.in","wd","x1.scf",0,tot_nsteps,1) # charged setupxdatcar2inp.xdatcar2inp("XDATCAR","x0.scf.in","wd","x0.scf",0,4,1)
# Step 2 - distribute all time steps into groups(jobs) # several time steps per group - this is to accelerate calculations# creates a "customized" submit file for each job and submit it - run# a swarm in independent calculations (trajectory pieces)# (HTC paradigm)# Provide the files below: # submit_templ.pbs - template for submit files - manually edit the variables# x.exp.in - file for export of the wavefunction
os.system("cp submit_templ.pbs wd")os.system("cp x0.exp.in wd")#os.system("cp x1.exp.in wd")os.chdir("wd")distribute.distribute(0,4,nsteps_per_job,"submit_templ.pbs",["x0.exp.in"],["x0.scf"],1) # 1 = PBS, 2 = SLURM, 0 = no run#distribute.distribute(0,tot_nsteps,nsteps_per_job,"submit_templ.pbs",["x0.exp.in","x1.exp.in"],["x0.scf","x1.scf"],1)
submit_templ.pbs,
在此输入代码...#!/bin/sh#PBS -l nodes=1:ppn=24
#PBS -N qe_test
#PBS -q q_zhq_bnulongr
cd $PBS_O_WORKDIR
NPROCS=$PBS_NP
source /home/export/parastor/clussoft/profile.d/intelmpi.sh
# mpirun -machinefile $PBS_NODEFILE -np $NPROCS pw.x <x.in> x.out
exe_qespresso=/home/export/parastor/keyuser/bnulongr/apps/qe/5.3.0/espresso-5.3.0/bin/pw.x
exe_export=/home/export/parastor/keyuser/bnulongr/apps/qe/5.3.0/espresso-5.3.0/bin/pw_export.x
exe_convert=/home/export/parastor/keyuser/bnulongr/apps/qe/5.3.0/espresso-5.3.0/bin/iotk
NP=$(wc -l $PBS_NODEFILE | awk '{print $1}')
res="/home/export/parastor/keyuser/bnulongr/apps/test/test2/res"
# These will be assigned automatically, leave them as they are
param1=
param2=
minband=176
# This is invocation of the scripts which will further handle NA-MD calclculations
# on the NAC calculation step
python -c "from PYXAID import *
params = { }
params[\"BATCH_SYSTEM\"]=\"mpirun\"
params[\"NP\"]=$NP
params[\"EXE\"]=\"$exe_qespresso\"
params[\"EXE_EXPORT\"]=\"$exe_export\"
params[\"EXE_CONVERT\"] =\"$exe_convert\"
params[\"start_indx\"]=$param1
params[\"stop_indx\"]=$param2
params[\"wd\"]=\"wd\"
params[\"rd\"]=\"$res\"
params[\"minband\"]=$minband
params[\"nocc\"]=176
params[\"maxband\"]=177
params[\"nac_method\"]=0
params[\"wfc_preprocess\"]=\"complete\"
params[\"do_complete\"]=1
params[\"prefix0\"]=\"x0.scf\"
params[\"compute_Hprime\"]=1
params[\"pptype\"]=\"US\"
print params
runMD1.runMD(params)
"
Best.
Misaraty
Wei Li
Sep 9, 2017, 3:52:42 AM9/9/17
to Quantum-Dynamics-Hub
Hi Misaraty,
Not enough information to say what is going wrong.
It seems your QE did not execute normally. Can you please post your QE input file? Or post the tail of x0.scf.x.out file.
Wei
misa...@gmail.com
Sep 9, 2017, 6:26:37 AM9/9/17
to Quantum-Dynamics-Hub
Hi Wei,
~/test0/wd/job0/wd/curr0/x0.scf.0.out
~/py-scr2.py,
Thanks.
I re-tested the pyxaid, qe seems to be no problem. Related content is as follows,
[bnulongr@sn21 test0]$ tree.├── py-scr2.py├── submit_templ.pbs├── wd│ ├── job0│ │ ├── CRASH│ │ ├── qe_test.e38391│ │ ├── qe_test.o38391│ │ ├── scf.save│ │ │ ├── charge-density.dat│ │ │ ├── C.pbe-rrkjus.UPF│ │ │ ├── data-file.xml│ │ │ ├── gvectors.dat│ │ │ ├── H.pbe-rrkjus.UPF│ │ │ ├── I.pbe-n-rrkjus_psl.0.2.UPF│ │ │ ├── K00001│ │ │ │ ├── eigenval.xml│ │ │ │ ├── evc.dat│ │ │ │ └── gkvectors.dat│ │ │ ├── N.pbe-rrkjus.UPF│ │ │ └── Pb.pbe-dn-rrkjus_psl.0.2.2.UPF│ │ ├── submit_templ.pbs│ │ ├── wd│ │ │ ├── curr0│ │ │ │ ├── x0.export│ │ │ │ └── x0.scf.0.out│ │ │ └── next0│ │ │ ├── x0.export│ │ │ └── x0.scf.1.out│ │ ├── x0.exp.in│ │ ├── x0.exp.out│ │ ├── x0.scf.0.in│ │ ├── x0.scf.1.in│ │ └── x0.scf.2.in│ ├── job1│ │ ├── CRASH│ │ ├── qe_test.e38392│ │ ├── qe_test.o38392│ │ ├── scf.save│ │ │ ├── charge-density.dat│ │ │ ├── C.pbe-rrkjus.UPF│ │ │ ├── data-file.xml│ │ │ ├── gvectors.dat│ │ │ ├── H.pbe-rrkjus.UPF│ │ │ ├── I.pbe-n-rrkjus_psl.0.2.UPF│ │ │ ├── K00001│ │ │ │ ├── eigenval.xml│ │ │ │ ├── evc.dat│ │ │ │ └── gkvectors.dat│ │ │ ├── N.pbe-rrkjus.UPF│ │ │ └── Pb.pbe-dn-rrkjus_psl.0.2.2.UPF│ │ ├── submit_templ.pbs│ │ ├── wd│ │ │ ├── curr0│ │ │ │ ├── x0.export│ │ │ │ └── x0.scf.2.out│ │ │ └── next0│ │ │ ├── x0.export│ │ │ └── x0.scf.3.out│ │ ├── x0.exp.in│ │ ├── x0.exp.out│ │ ├── x0.scf.2.in│ │ └── x0.scf.3.in│ ├── submit_templ.pbs│ ├── tmp│ ├── x0.exp.in│ ├── x0.scf.0.in│ ├── x0.scf.1.in│ ├── x0.scf.2.in│ ├── x0.scf.3.in│ └── x0.scf.4.in├── x0.exp.in├── x0.scf.in└── XDATCAR
17 directories, 56 files~/test0/wd/job0/wd/curr0/x0.scf.0.out
Program PWSCF v.5.3.0 (svn rev. 11974) starts on 9Sep2017 at 18: 0:10
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); in publications or presentations arising from this work. More details at
Parallel version (MPI), running on 12 processors R & G space division: proc/nbgrp/npool/nimage = 12 Waiting for input... Reading input from standard inputWarning: card &IONS ignoredWarning: card ION_DYNAMICS = 'VERLET', ignoredWarning: card ION_TEMPERATURE = 'ANDERSEN', ignoredWarning: card TEMPW = 300.00 , ignoredWarning: card NRAISE = 1, ignoredWarning: card / ignored Message from routine read_cards : DEPRECATED: no units specified in CELL_PARAMETERS card
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) = 3 file C.pbe-rrkjus.UPF: wavefunction(s) 2S 2P renormalized file N.pbe-rrkjus.UPF: wavefunction(s) 2S renormalized file H.pbe-rrkjus.UPF: wavefunction(s) 1S renormalized file Pb.pbe-dn-rrkjus_psl.0.2.2.UPF: wavefunction(s) 6S renormalized
gamma-point specific algorithms are used
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 1149 614 153 101593 39566 4945 Max 1152 616 156 101604 39644 4950 Sum 13809 7377 1853 1219157 475273 59373 Tot 6905 3689 927
bravais-lattice index = 0 lattice parameter (alat) = 1.8897 a.u. unit-cell volume = 13896.6342 (a.u.)^3 number of atoms/cell = 96 number of atomic types = 5 number of electrons = 432.00 number of Kohn-Sham states= 259 kinetic-energy cutoff = 40.0000 Ry charge density cutoff = 300.0000 Ry convergence threshold = 1.0E-05 mixing beta = 0.4500 number of iterations used = 8 plain mixing Exchange-correlation = PBE ( 1 4 3 4 0 0)
celldm(1)= 1.889700 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) = ( 12.722600 0.000000 0.000000 ) a(2) = ( 0.000000 12.722600 0.000000 ) a(3) = ( 0.000000 0.000000 12.722700 )
reciprocal axes: (cart. coord. in units 2 pi/alat) b(1) = ( 0.078600 0.000000 0.000000 ) b(2) = ( 0.000000 0.078600 0.000000 ) b(3) = ( 0.000000 0.000000 0.078600 )
PseudoPot. # 1 for C read from file: /home/export/parastor/keyuser/bnulongr/soft/qe/upf_files/C.pbe-rrkjus.UPF MD5 check sum: 00fb224312de0c5b6853bd333518df6f Pseudo is Ultrasoft, Zval = 4.0 Generated by new atomic code, or converted to UPF format Using radial grid of 627 points, 4 beta functions with: l(1) = 0 l(2) = 0 l(3) = 1 l(4) = 1 Q(r) pseudized with 0 coefficients
PseudoPot. # 2 for N read from file: /home/export/parastor/keyuser/bnulongr/soft/qe/upf_files/N.pbe-rrkjus.UPF MD5 check sum: 0c3fbe5807a93f9ba59d5a7019aa238b Pseudo is Ultrasoft, Zval = 5.0 Generated by new atomic code, or converted to UPF format Using radial grid of 1257 points, 4 beta functions with: l(1) = 0 l(2) = 0 l(3) = 1 l(4) = 1 Q(r) pseudized with 0 coefficients
PseudoPot. # 3 for H read from file: /home/export/parastor/keyuser/bnulongr/soft/qe/upf_files/H.pbe-rrkjus.UPF MD5 check sum: 7cc9d459525c9a0585f487a71c3c9563 Pseudo is Ultrasoft, Zval = 1.0 Generated by new atomic code, or converted to UPF format Using radial grid of 1061 points, 2 beta functions with: l(1) = 0 l(2) = 0 Q(r) pseudized with 0 coefficients
PseudoPot. # 4 for Pb read from file: /home/export/parastor/keyuser/bnulongr/soft/qe/upf_files/Pb.pbe-dn-rrkjus_psl.0.2.2.UPF MD5 check sum: 7afc420059c37d6888fc09c0f121e83f Pseudo is Ultrasoft + core correction, Zval = 14.0 Generated using "atomic" code by A. Dal Corso v.5.0.2 svn rev. 9415 Using radial grid of 1281 points, 6 beta functions with: l(1) = 0 l(2) = 0 l(3) = 1 l(4) = 1 l(5) = 2 l(6) = 2 Q(r) pseudized with 0 coefficients
PseudoPot. # 5 for I read from file: /home/export/parastor/keyuser/bnulongr/soft/qe/upf_files/I.pbe-n-rrkjus_psl.0.2.UPF MD5 check sum: f9a5bb98cc7d7d8a1a5c1f9867e5ab3f Pseudo is Ultrasoft + core correction, Zval = 7.0 Generated using "atomic" code by A. Dal Corso v.5.0.2 svn rev. 9415 Using radial grid of 1247 points, 4 beta functions with: l(1) = 0 l(2) = 0 l(3) = 1 l(4) = 1 Q(r) pseudized with 0 coefficients
atomic species valence mass pseudopotential C 4.00 12.01000 C ( 1.00) N 5.00 14.00700 N ( 1.00) H 1.00 1.00800 H ( 1.00) Pb 14.00 207.20000 Pb( 1.00) I 7.00 126.90400 I( 1.00)
No symmetry found
Cartesian axes
site n. atom positions (alat units) 1 C tau( 1) = ( 12.4919900 0.0400400 1.0058100 ) 2 C tau( 2) = ( 6.8445800 12.4877400 12.5842900 ) 3 C tau( 3) = ( 12.4829700 0.2653700 7.0510000 ) 4 C tau( 4) = ( 5.9233800 0.3575200 7.2043300 ) 5 C tau( 5) = ( 0.1250700 6.5634400 0.8483900 ) 6 C tau( 6) = ( 6.2863700 6.5229000 12.4244900 ) 7 C tau( 7) = ( 0.4100500 6.2821900 6.8020300 ) 8 C tau( 8) = ( 6.4432300 7.1875000 6.0918700 ) 9 N tau( 9) = ( 0.8430100 0.6802900 0.5738100 ) 10 N tau( 10) = ( 11.5096300 12.3539500 0.2314700 ) 11 N tau( 11) = ( 6.7262100 0.0723700 11.3086400 ) 12 N tau( 12) = ( 5.8857600 12.5626800 0.7883300 ) 13 N tau( 13) = ( 0.6778100 12.1259500 7.4620200 ) 14 N tau( 14) = ( 11.9832300 0.3638500 5.8549500 ) 15 N tau( 15) = ( 7.0612600 0.1295700 6.5855000 ) 16 N tau( 16) = ( 4.7662900 0.1612000 6.6382000 ) 17 N tau( 17) = ( 1.1951700 6.6842000 0.0913500 ) 18 N tau( 18) = ( 11.6594000 6.4806600 0.3205100 ) 19 N tau( 19) = ( 6.4000600 5.3831700 0.4042000 ) 20 N tau( 20) = ( 6.3446300 6.6490700 11.1241500 ) 21 N tau( 21) = ( 12.4083300 6.7449400 5.7790400 ) 22 N tau( 22) = ( 0.2324200 5.1396800 7.4611100 ) 23 N tau( 23) = ( 7.4716900 6.3766100 6.3276800 ) 24 N tau( 24) = ( 5.1948900 6.8346400 6.3042500 ) 25 H tau( 25) = ( 12.4100900 12.4852800 2.1023200 ) 26 H tau( 26) = ( 1.5554400 0.9869600 1.2502900 ) 27 H tau( 27) = ( 0.9541800 1.0052400 12.3382000 ) 28 H tau( 28) = ( 11.5191400 12.5474300 11.9365700 ) 29 H tau( 29) = ( 10.6787900 11.8952600 0.6746000 ) 30 H tau( 30) = ( 7.7872900 12.1539800 0.1774700 ) 31 H tau( 31) = ( 7.4926200 12.5420300 10.6460100 ) 32 H tau( 32) = ( 5.8187800 0.2817400 10.9233000 ) 33 H tau( 33) = ( 5.0280700 0.3262800 0.5673300 ) 34 H tau( 34) = ( 6.1082700 12.3477300 1.7655300 ) 35 H tau( 35) = ( 12.0403300 0.8925300 7.7828200 ) 36 H tau( 36) = ( 1.1000700 12.1904200 8.4263000 ) 37 H tau( 37) = ( 1.1950400 11.5481600 6.7764400 ) 38 H tau( 38) = ( 12.2673900 12.4806200 5.0699900 ) 39 H tau( 39) = ( 11.2814700 1.1212900 5.6690400 ) 40 H tau( 40) = ( 5.9952700 0.7481000 8.2662700 ) 41 H tau( 41) = ( 7.9357100 0.0972200 7.1242400 ) 42 H tau( 42) = ( 7.0549700 12.3478700 5.6921700 ) 43 H tau( 43) = ( 4.6324600 12.5303300 5.6896700 ) 44 H tau( 44) = ( 3.9060800 0.4232400 7.1092200 ) 45 H tau( 45) = ( 0.2367600 6.5795200 2.0155700 ) 46 H tau( 46) = ( 2.1361900 6.6418900 0.5132700 ) 47 H tau( 47) = ( 1.1429500 6.5800800 11.8158400 ) 48 H tau( 48) = ( 11.4945200 6.4741600 12.0050800 ) 49 H tau( 49) = ( 10.8291400 6.4629900 0.9355400 ) 50 H tau( 50) = ( 6.2125500 7.4204200 0.2415600 ) 51 H tau( 51) = ( 6.2397100 5.4677200 1.4095900 ) 52 H tau( 52) = ( 6.3722200 4.4447400 12.6953900 ) 53 H tau( 53) = ( 6.3630500 5.7988000 10.5171500 ) 54 H tau( 54) = ( 6.2603300 7.5964600 10.7267700 ) 55 H tau( 55) = ( 1.1620900 6.9168700 7.1774400 ) 56 H tau( 56) = ( 12.6795300 7.5598700 5.2132000 ) 57 H tau( 57) = ( 11.7710300 6.0875000 5.2293900 ) 58 H tau( 58) = ( 12.2900800 4.4318200 7.0855300 ) 59 H tau( 59) = ( 0.8537100 4.8448800 8.2313000 ) 60 H tau( 60) = ( 6.7080500 8.2799200 5.7069400 ) 61 H tau( 61) = ( 8.4394700 6.6725100 6.1645600 ) 62 H tau( 62) = ( 7.2923000 5.4071700 6.6036600 ) 63 H tau( 63) = ( 4.9657300 5.8822300 6.6250100 ) 64 H tau( 64) = ( 4.3937100 7.4687800 6.1901900 ) 65 Pb tau( 65) = ( 3.3223100 3.0330200 3.1343400 ) 66 Pb tau( 66) = ( 9.4883700 2.8055200 2.8622300 ) 67 Pb tau( 67) = ( 2.8652400 3.0038800 9.4851000 ) 68 Pb tau( 68) = ( 9.4333700 2.8068100 9.2205000 ) 69 Pb tau( 69) = ( 3.0607500 9.2176100 2.6108500 ) 70 Pb tau( 70) = ( 9.3284100 9.3833700 2.9170100 ) 71 Pb tau( 71) = ( 3.1973400 9.6238800 9.0181600 ) 72 Pb tau( 72) = ( 10.1182900 8.7738400 9.1584900 ) 73 I tau( 73) = ( 0.0736100 3.9516400 3.1730600 ) 74 I tau( 74) = ( 2.5400000 0.1736600 3.9222500 ) 75 I tau( 75) = ( 3.9132200 2.5425700 0.1036600 ) 76 I tau( 76) = ( 6.5502800 3.2752500 3.6722500 ) 77 I tau( 77) = ( 9.6405100 12.5064500 3.4155500 ) 78 I tau( 78) = ( 9.1756100 2.3590800 12.4907900 ) 79 I tau( 79) = ( 12.7091900 3.4476900 10.5446600 ) 80 I tau( 80) = ( 3.2117300 0.1387300 10.2090300 ) 81 I tau( 81) = ( 2.9787200 3.7375100 6.3680700 ) 82 I tau( 82) = ( 6.4285700 3.4771200 9.0660700 ) 83 I tau( 83) = ( 9.5584600 12.4561500 9.5372700 ) 84 I tau( 84) = ( 9.9466000 3.3302100 5.9067700 ) 85 I tau( 85) = ( 12.6327800 9.6750400 3.5477800 ) 86 I tau( 86) = ( 3.7782600 6.3580300 3.2901300 ) 87 I tau( 87) = ( 4.1346700 9.6924300 12.5078800 ) 88 I tau( 88) = ( 6.2929300 10.2429500 3.7867000 ) 89 I tau( 89) = ( 9.5942700 6.4656000 3.6355600 ) 90 I tau( 90) = ( 8.2797700 9.6649500 12.6198300 ) 91 I tau( 91) = ( 12.7128000 9.7931200 10.3346000 ) 92 I tau( 92) = ( 2.9643000 6.5013900 9.4788700 ) 93 I tau( 93) = ( 3.1393000 9.6313300 5.9390600 ) 94 I tau( 94) = ( 6.1648500 10.0217400 9.0935100 ) 95 I tau( 95) = ( 9.9499700 5.9194300 10.2464200 ) 96 I tau( 96) = ( 9.3139500 9.7968000 6.1221900 )
number of k points= 1 gaussian smearing, width (Ry)= 0.0050 cart. coord. in units 2pi/alat k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 2.0000000
Dense grid: 609579 G-vectors FFT dimensions: ( 135, 135, 135)
Smooth grid: 237637 G-vectors FFT dimensions: ( 100, 100, 100)
Largest allocated arrays est. size (Mb) dimensions Kohn-Sham Wavefunctions 9.78 Mb ( 2475, 259) NL pseudopotentials 22.96 Mb ( 2475, 608) Each V/rho on FFT grid 3.34 Mb ( 218700) Each G-vector array 0.39 Mb ( 50799) G-vector shells 0.16 Mb ( 21160) Largest temporary arrays est. size (Mb) dimensions Auxiliary wavefunctions 19.56 Mb ( 2475, 1036) Each subspace H/S matrix 8.19 Mb ( 1036, 1036) Each <psi_i|beta_j> matrix 1.20 Mb ( 608, 259) Arrays for rho mixing 26.70 Mb ( 218700, 8)
Initial potential from superposition of free atoms
starting charge 428.13062, renormalised to 432.00000 Starting wfc are 304 randomized atomic wfcs
total cpu time spent up to now is 13.8 secs
per-process dynamical memory: 119.8 Mb
Self-consistent Calculation
iteration # 1 ecut= 40.00 Ry beta=0.45 Davidson diagonalization with overlap ethr = 1.00E-02, avg # of iterations = 5.0
total cpu time spent up to now is 42.1 secs
total energy = -3025.42578700 Ry Harris-Foulkes estimate = -3059.45176516 Ry estimated scf accuracy < 53.47385667 Ry
iteration # 2 ecut= 40.00 Ry beta=0.45 Davidson diagonalization with overlap ethr = 1.00E-02, avg # of iterations = 5.0
total cpu time spent up to now is 70.9 secs
total energy = -3036.96864618 Ry Harris-Foulkes estimate = -3054.27057340 Ry estimated scf accuracy < 46.11759532 Ry
iteration # 3 ecut= 40.00 Ry beta=0.45 Davidson diagonalization with overlap ethr = 1.00E-02, avg # of iterations = 2.0
total cpu time spent up to now is 89.6 secs
total energy = -3046.35043786 Ry Harris-Foulkes estimate = -3047.28252385 Ry estimated scf accuracy < 3.04620659 Ry
iteration # 4 ecut= 40.00 Ry beta=0.45 Davidson diagonalization with overlap ethr = 7.05E-04, avg # of iterations = 5.0
total cpu time spent up to now is 115.2 secs
total energy = -3046.54314178 Ry Harris-Foulkes estimate = -3046.75265758 Ry estimated scf accuracy < 0.61165556 Ry
iteration # 5 ecut= 40.00 Ry beta=0.45 Davidson diagonalization with overlap ethr = 1.42E-04, avg # of iterations = 3.0
total cpu time spent up to now is 136.7 secs
total energy = -3046.60397934 Ry Harris-Foulkes estimate = -3046.63668807 Ry estimated scf accuracy < 0.10598924 Ry
iteration # 6 ecut= 40.00 Ry beta=0.45 Davidson diagonalization with overlap ethr = 2.45E-05, avg # of iterations = 7.0
total cpu time spent up to now is 161.7 secs
total energy = -3046.61692321 Ry Harris-Foulkes estimate = -3046.62183164 Ry estimated scf accuracy < 0.02018780 Ry
iteration # 7 ecut= 40.00 Ry beta=0.45 Davidson diagonalization with overlap ethr = 4.67E-06, avg # of iterations = 11.0
total cpu time spent up to now is 189.1 secs
total energy = -3046.61962115 Ry Harris-Foulkes estimate = -3046.62001181 Ry estimated scf accuracy < 0.00178714 Ry
iteration # 8 ecut= 40.00 Ry beta=0.45 Davidson diagonalization with overlap ethr = 4.14E-07, avg # of iterations = 3.0
total cpu time spent up to now is 213.1 secs
total energy = -3046.62001751 Ry Harris-Foulkes estimate = -3046.62010963 Ry estimated scf accuracy < 0.00050524 Ry
iteration # 9 ecut= 40.00 Ry beta=0.45 Davidson diagonalization with overlap ethr = 1.17E-07, avg # of iterations = 2.0
total cpu time spent up to now is 233.3 secs
total energy = -3046.62008352 Ry Harris-Foulkes estimate = -3046.62009707 Ry estimated scf accuracy < 0.00014802 Ry
iteration # 10 ecut= 40.00 Ry beta=0.45 Davidson diagonalization with overlap ethr = 3.43E-08, avg # of iterations = 2.0
total cpu time spent up to now is 254.2 secs
total energy = -3046.62010510 Ry Harris-Foulkes estimate = -3046.62010449 Ry estimated scf accuracy < 0.00002471 Ry
iteration # 11 ecut= 40.00 Ry beta=0.45 Davidson diagonalization with overlap ethr = 5.72E-09, avg # of iterations = 2.0
total cpu time spent up to now is 277.1 secs
End of self-consistent calculation
k = 0.0000 0.0000 0.0000 ( 29687 PWs) bands (ev):
-18.0521 -18.0342 -17.9534 -17.8608 -17.6900 -17.6488 -17.5557 -17.2922 -15.8147 -15.6955 -15.6220 -15.5481 -15.5402 -15.4460 -15.3875 -15.1642 -14.6231 -14.5936 -14.5750 -14.5328 -14.5030 -14.4460 -14.4392 -14.4264 -14.4146 -14.4120 -14.4067 -14.3966 -14.3703 -14.3571 -14.3272 -14.2205 -14.1947 -14.1753 -14.1744 -14.1580 -14.1560 -14.1358 -14.1283 -14.1023 -14.0959 -14.0847 -14.0712 -14.0518 -14.0437 -14.0323 -13.9780 -13.9713 -13.9522 -13.9413 -13.9241 -13.8336 -13.8107 -13.7891 -13.7819 -13.7632 -9.9307 -9.8420 -9.7400 -9.7243 -9.6716 -9.5629 -9.5510 -9.4889 -9.4665 -9.3916 -9.3479 -9.3411 -9.2823 -9.2677 -9.2212 -9.1849 -9.1701 -9.1596 -9.0397 -9.0072 -8.9887 -8.9138 -8.8789 -8.8628 -8.8318 -8.7661 -8.7317 -8.6846 -8.6788 -8.5838 -8.4552 -8.3821 -7.8747 -7.8005 -7.6743 -7.6613 -7.6406 -7.5340 -7.4401 -7.2534 -7.2387 -7.1005 -7.0694 -6.9964 -6.8699 -6.7726 -6.7397 -6.5595 -5.7529 -5.5396 -5.4560 -5.3951 -5.3841 -5.3419 -5.3271 -5.3028 -5.2928 -5.2390 -5.2112 -5.0880 -5.0158 -4.9080 -4.8042 -4.5879 -4.0928 -3.9205 -3.8523 -3.7788 -3.7439 -3.7008 -3.5687 -3.5359 -3.3982 -3.3739 -3.3207 -3.3169 -3.1652 -3.1315 -3.0836 -2.8016 -0.9536 -0.7925 -0.7561 -0.6331 -0.5817 -0.5111 -0.4818 -0.4595 -0.4206 -0.3107 -0.2932 -0.2223 -0.2196 -0.1772 -0.1241 -0.1172 -0.0503 -0.0156 0.0533 0.1332 0.2054 0.2313 0.3285 0.4526 0.4783 0.5197 0.5371 0.5832 0.5910 0.6685 0.6913 0.7505 0.8137 0.8296 0.8498 0.8716 0.9087 0.9280 0.9516 0.9786 1.0149 1.0524 1.0734 1.1206 1.1464 1.1857 1.2238 1.2402 1.2750 1.2894 1.3189 1.3341 1.3685 1.3886 1.4104 1.4648 1.5120 1.5188 1.5346 1.5982 1.6212 1.6384 1.6598 1.6844 1.6900 1.7464 1.7557 1.7723 1.8115 1.8527 1.8830 1.9464 1.9717 1.9988 2.0258 2.0473 2.0971 2.1412 2.2443 2.2874 4.1588 4.3119 4.3533 4.4116 4.4309 4.6307 4.7539 4.7964 4.8986 4.9889 5.0700 5.1133 5.2301 5.2728 5.4010 5.4413 5.4626 5.5621 5.5800 5.6566 5.8258 5.8745 5.9663 6.1086 6.2079 6.3749 6.4530 6.5068 6.6329 6.7235 6.8843 6.9062 7.0223 7.1603 7.2420 7.2896 7.3807 7.4608 7.5092 7.5675 7.6429 7.7140 7.7466
the Fermi energy is 2.9944 ev
! total energy = -3046.62010819 Ry Harris-Foulkes estimate = -3046.62011082 Ry estimated scf accuracy < 0.00000440 Ry
The total energy is the sum of the following terms:
one-electron contribution = -1006.61785163 Ry hartree contribution = 677.20464798 Ry xc contribution = -1496.32419759 Ry ewald contribution = -1220.88270695 Ry smearing contrib. (-TS) = -0.00000000 Ry
convergence has been achieved in 11 iterations
Writing output data file scf.save
init_run : 12.74s CPU 12.93s WALL ( 1 calls) electrons : 257.54s CPU 263.42s WALL ( 1 calls)
Called by init_run: wfcinit : 5.25s CPU 5.32s WALL ( 1 calls) potinit : 2.78s CPU 2.82s WALL ( 1 calls)
Called by electrons: c_bands : 216.69s CPU 220.67s WALL ( 11 calls) sum_band : 28.36s CPU 29.37s WALL ( 11 calls) v_of_rho : 3.32s CPU 3.47s WALL ( 12 calls) newd : 9.20s CPU 9.85s WALL ( 12 calls) mix_rho : 0.47s CPU 0.48s WALL ( 11 calls)
Called by c_bands: init_us_2 : 0.22s CPU 0.24s WALL ( 23 calls) regterg : 215.75s CPU 219.70s WALL ( 11 calls)
Called by sum_band: sum_band:bec : 0.02s CPU 0.02s WALL ( 11 calls) addusdens : 9.99s CPU 10.65s WALL ( 11 calls)
Called by *egterg: h_psi : 80.92s CPU 82.18s WALL ( 59 calls) s_psi : 32.03s CPU 32.68s WALL ( 59 calls) g_psi : 0.07s CPU 0.07s WALL ( 47 calls) rdiaghg : 24.47s CPU 24.74s WALL ( 58 calls)
Called by h_psi: add_vuspsi : 31.76s CPU 32.29s WALL ( 59 calls)
General routines calbec : 45.45s CPU 46.12s WALL ( 70 calls) fft : 3.19s CPU 3.28s WALL ( 188 calls) ffts : 0.10s CPU 0.11s WALL ( 23 calls) fftw : 17.26s CPU 17.53s WALL ( 8878 calls) interpolate : 0.51s CPU 0.54s WALL ( 23 calls)
Parallel routines fft_scatter : 5.74s CPU 5.60s WALL ( 9089 calls)
PWSCF : 4m31.26s CPU 4m38.14s WALL
This run was terminated on: 18: 4:48 9Sep2017
=------------------------------------------------------------------------------= JOB DONE.=------------------------------------------------------------------------------=
~/py-scr2.py,
from PYXAID import *import os
nsteps_per_job = 2tot_nsteps = 4
# os.system("rm -rf wd")
# Step 1 - split MD trajectory on the time steps# Provide files listed below: "x.md.out" and "x.scf.in"# IMPORTANT: # 1) use only ABSOLUTE path for PP in x.scf.in file# 2) provided input file is just a template, so do not include coordinates#out2inp.out2inp("x.md.out","x0.scf.in","wd","x0.scf",0,tot_nsteps,1) # neutral setup#out2inp.out2inp("x.md.out","x1.scf.in","wd","x1.scf",0,tot_nsteps,1) # charged setupxdatcar2inp.xdatcar2inp("XDATCAR","x0.scf.in","wd","x0.scf",0,4,1)
# Step 2 - distribute all time steps into groups(jobs) # several time steps per group - this is to accelerate calculations# creates a "customized" submit file for each job and submit it - run# a swarm in independent calculations (trajectory pieces)# (HTC paradigm)# Provide the files below: # submit_templ.pbs - template for submit files - manually edit the variables# x.exp.in - file for export of the wavefunction
os.system("cp submit_templ.pbs wd")os.system("cp x0.exp.in wd")#os.system("cp x1.exp.in wd")os.chdir("wd")distribute.distribute(0,4,nsteps_per_job,"submit_templ.pbs",["x0.exp.in"],["x0.scf"],1) # 1 = PBS, 2 = SLURM, 0 = no run#distribute.distribute(0,tot_nsteps,nsteps_per_job,"submit_templ.pbs",["x0.exp.in","x1.exp.in"],["x0.scf","x1.scf"],1)
~/submit_templ.pbs,
#!/bin/sh
#PBS -l nodes=1:ppn=12#PBS -N qe_test#PBS -q q_zhq_bnulongr
cd $PBS_O_WORKDIR
NPROCS=$PBS_NP
source /home/export/parastor/clussoft/profile.d/intelmpi.sh # mpirun -machinefile $PBS_NODEFILE -np $NPROCS pw.x <x.in> x.out
exe_qespresso=/home/export/parastor/keyuser/bnulongr/apps/qe/5.3.0/espresso-5.3.0/bin/pw.xexe_export=/home/export/parastor/keyuser/bnulongr/apps/qe/5.3.0/espresso-5.3.0/bin/pw_export.xexe_convert=/home/export/parastor/keyuser/bnulongr/apps/qe/5.3.0/espresso-5.3.0/bin/iotk
NP=$(wc -l $PBS_NODEFILE | awk '{print $1}')res=/home/export/parastor/keyuser/bnulongr/works/test/test0/res&inputpp prefix = 'x0', outdir = './', pseudo_dir = '/home/export/parastor/keyuser/bnulongr/soft/qe/upf_files', psfile(1) = 'C.pbe-rrkjus.UPF', psfile(2) = 'N.pbe-rrkjus.UPF', psfile(3) = 'H.pbe-rrkjus.UPF', psfile(4) = 'Pb.pbe-dn-kjpaw_psl.0.2.2.UPF' psfile(5) = 'I.pbe-n-kjpaw_psl.0.2.UPF', single_file = .FALSE., ascii = .TRUE., uspp_spsi = .FALSE.,/&CONTROL calculation = 'scf', pseudo_dir = '/home/export/parastor/keyuser/bnulongr/soft/qe/upf_files', outdir = './', prefix = 'scf', disk_io = 'low', wf_collect = .true./
&SYSTEM ibrav = 0, celldm(1) = 1.8897, nat = 96, ntyp = 5,! nspin = 2,! nbnd = 20, ecutwfc = 40.D0, ecutrho = 300.D0,! tot_charge = 0.0,! starting_magnetization(1) = 0.01 !do the spin polarized calculation to get the wfc1,2,etc files occupations = 'smearing', smearing = 'gaussian', degauss = 0.005, nosym = .true.,/
&ELECTRONS electron_maxstep = 300, conv_thr = 1.D-5, mixing_beta = 0.45,/
&IONS ion_dynamics = 'verlet', ion_temperature = 'andersen', tempw = 300.00 , nraise = 1,/
ATOMIC_SPECIES C 12.01 C.pbe-rrkjus.UPF N 14.0069999695 N.pbe-rrkjus.UPF H 1.008 H.pbe-rrkjus.UPFPb 207.1999969482 Pb.pbe-dn-rrkjus_psl.0.2.2.UPFI 126.9039993286 I.pbe-n-rrkjus_psl.0.2.UPF
K_POINTS gamma CELL_PARAMETERS 12.7225999832000003 0.0000000000000000 0.0000000000000000 0.0000000000000000 12.7225999832000003 0.0000000000000000 0.0000000000000000 0.0000000000000000 12.7227001190000006Misaraty
misa...@gmail.com
Sep 9, 2017, 8:00:58 AM9/9/17
to Quantum-Dynamics-Hub
Hi Wei,
Thanks.
According to your opinion, I have modified the prefix = x0 in x0.exp.in and x0.scf.in, but did not generate the _re and _im in res folder.
[bnulongr@sn21 test0]$ tree.├── py-scr2.py├── submit_templ.pbs├── wd│ ├── job0│ │ ├── qe_test.e38395│ │ ├── qe_test.o38395│ │ ├── submit_templ.pbs│ │ ├── wd│ │ │ └── curr0│ │ │ ├── x0.export│ │ │ │ ├── grid.1│ │ │ │ ├── index.xml│ │ │ │ ├── mgrid│ │ │ │ ├── wfc.1│ │ │ │ └── wfc.1.xml│ │ │ ├── x0.scf.2.out│ │ │ ├── x0.wfc1│ │ │ ├── x0.wfc10│ │ │ ├── x0.wfc11│ │ │ ├── x0.wfc12│ │ │ ├── x0.wfc2│ │ │ ├── x0.wfc3│ │ │ ├── x0.wfc4│ │ │ ├── x0.wfc5│ │ │ ├── x0.wfc6│ │ │ ├── x0.wfc7│ │ │ ├── x0.wfc8│ │ │ └── x0.wfc9│ │ ├── x0.exp.in│ │ ├── x0.exp.out│ │ ├── x0.save│ │ │ ├── charge-density.dat│ │ │ ├── C.pbe-rrkjus.UPF│ │ │ ├── data-file.xml│ │ │ ├── gvectors.dat│ │ │ ├── H.pbe-rrkjus.UPF│ │ │ ├── I.pbe-n-rrkjus_psl.0.2.UPF│ │ │ ├── K00001│ │ │ │ ├── eigenval.xml│ │ │ │ ├── evc.dat│ │ │ │ └── gkvectors.dat│ │ │ ├── N.pbe-rrkjus.UPF│ │ │ └── Pb.pbe-dn-rrkjus_psl.0.2.2.UPF│ │ ├── x0.scf.0.in│ │ ├── x0.scf.1.in│ │ └── x0.scf.2.in│ ├── job1│ │ ├── qe_test.e38396│ │ ├── qe_test.o38396│ │ ├── submit_templ.pbs│ │ ├── wd│ │ │ └── curr0│ │ │ ├── x0.export│ │ │ │ ├── grid.1│ │ │ │ ├── index.xml│ │ │ │ ├── mgrid│ │ │ │ ├── wfc.1│ │ │ │ └── wfc.1.xml│ │ │ ├── x0.scf.3.out│ │ │ ├── x0.wfc1│ │ │ ├── x0.wfc10│ │ │ ├── x0.wfc11│ │ │ ├── x0.wfc12│ │ │ ├── x0.wfc2│ │ │ ├── x0.wfc3│ │ │ ├── x0.wfc4│ │ │ ├── x0.wfc5│ │ │ ├── x0.wfc6│ │ │ ├── x0.wfc7│ │ │ ├── x0.wfc8│ │ │ └── x0.wfc9│ │ ├── x0.exp.in│ │ ├── x0.exp.out│ │ ├── x0.save│ │ │ ├── charge-density.dat│ │ │ ├── C.pbe-rrkjus.UPF│ │ │ ├── data-file.xml│ │ │ ├── gvectors.dat│ │ │ ├── H.pbe-rrkjus.UPF│ │ │ ├── I.pbe-n-rrkjus_psl.0.2.UPF│ │ │ ├── K00001│ │ │ │ ├── eigenval.xml│ │ │ │ ├── evc.dat│ │ │ │ └── gkvectors.dat│ │ │ ├── N.pbe-rrkjus.UPF│ │ │ └── Pb.pbe-dn-rrkjus_psl.0.2.2.UPF│ │ ├── x0.scf.2.in│ │ └── x0.scf.3.in│ ├── submit_templ.pbs│ ├── tmp│ ├── x0.exp.in│ ├── x0.scf.0.in│ ├── x0.scf.1.in│ ├── x0.scf.2.in│ ├── x0.scf.3.in│ └── x0.scf.4.in├── x0.exp.in├── x0.scf.in└── XDATCAR
13 directories, 86 filesAt the same time, I tested the official example again and there was the same problem,
[bnulongr@sn21 test3]$ tree.├── py-scr2.py├── py-scr6.py├── py-scr7.py├── res.tar.bz2├── spectr.tar.bz2├── submit.pbs├── submit_templ.pbs├── submit_templ.slm├── wd│ ├── job0│ │ ├── qe_test.e38388│ │ ├── qe_test.o38388│ │ ├── submit_templ.pbs│ │ ├── wd_test│ │ │ └── curr0│ │ │ ├── x0.export│ │ │ │ ├── grid.1│ │ │ │ ├── grid.2│ │ │ │ ├── index.xml│ │ │ │ ├── mgrid│ │ │ │ ├── wfc.1│ │ │ │ ├── wfc.1.xml│ │ │ │ └── wfc.2│ │ │ ├── x0.scf.2.out│ │ │ └── x0.wfc1│ │ ├── x0.exp.in│ │ ├── x0.exp.out│ │ ├── x0.save│ │ │ ├── charge-density.dat│ │ │ ├── C.pbe-rrkjus.UPF│ │ │ ├── data-file.xml│ │ │ ├── gvectors.dat│ │ │ ├── H.pbe-rrkjus.UPF│ │ │ ├── K00001│ │ │ │ ├── eigenval1.xml│ │ │ │ ├── eigenval2.xml│ │ │ │ ├── evc1.dat│ │ │ │ ├── evc2.dat│ │ │ │ └── gkvectors.dat│ │ │ └── spin-polarization.dat│ │ ├── x0.scf.0.in│ │ ├── x0.scf.1.in│ │ └── x0.scf.2.in│ ├── job1│ │ ├── qe_test.e38389│ │ ├── qe_test.o38389│ │ ├── submit_templ.pbs│ │ ├── wd_test│ │ │ └── curr0│ │ │ ├── x0.export│ │ │ │ ├── grid.1│ │ │ │ ├── grid.2│ │ │ │ ├── index.xml│ │ │ │ ├── mgrid│ │ │ │ ├── wfc.1│ │ │ │ ├── wfc.1.xml│ │ │ │ └── wfc.2│ │ │ ├── x0.scf.3.out│ │ │ └── x0.wfc1│ │ ├── x0.exp.in│ │ ├── x0.exp.out│ │ ├── x0.save│ │ │ ├── charge-density.dat│ │ │ ├── C.pbe-rrkjus.UPF│ │ │ ├── data-file.xml│ │ │ ├── gvectors.dat│ │ │ ├── H.pbe-rrkjus.UPF│ │ │ ├── K00001│ │ │ │ ├── eigenval1.xml│ │ │ │ ├── eigenval2.xml│ │ │ │ ├── evc1.dat│ │ │ │ ├── evc2.dat│ │ │ │ └── gkvectors.dat│ │ │ └── spin-polarization.dat│ │ ├── x0.scf.2.in│ │ └── x0.scf.3.in│ ├── submit_templ.pbs│ ├── tmp│ ├── x0.exp.in│ ├── x0.scf.0.in│ ├── x0.scf.1.in│ ├── x0.scf.2.in│ ├── x0.scf.3.in│ └── x0.scf.4.in├── x0.exp.in├── x0.scf.in└── x.md.out
13 directories, 74 filessubmit.pbs,
#!/bin/sh
#PBS -l nodes=1:ppn=2#PBS -N qe_test#PBS -q q_zhq_bnulongr
# cd $PBS_O_WORKDIR
# NPROCS=$PBS_NP
source /home/export/parastor/clussoft/profile.d/intelmpi.sh # mpirun -machinefile $PBS_NODEFILE -np $NPROCS pw.x <x.in> x.out
exe_qespresso=/home/export/parastor/keyuser/bnulongr/apps/qe/5.3.0/espresso-5.3.0/bin/pw.xexe_export=/home/export/parastor/keyuser/bnulongr/apps/qe/5.3.0/espresso-5.3.0/bin/pw_export.xexe_convert=/home/export/parastor/keyuser/bnulongr/apps/qe/5.3.0/espresso-5.3.0/bin/iotk
res=/home/export/parastor/keyuser/bnulongr/apps/test/test3/res
# These will be assigned automatically, leave them as they areparam1=param2=
# This is invocation of the scripts which will further handle NA-MD calclculations# on the NAC calculation steppython -c "from PYXAID import *params = { }params[\"NP\"]=$NPparams[\"EXE\"]=\"$exe_qespresso\"params[\"EXE_EXPORT\"]=\"$exe_export\"params[\"EXE_CONVERT\"] = \"$exe_convert\"params[\"start_indx\"]=$param1params[\"stop_indx\"]=$param2params[\"wd\"]=\"wd_test\"params[\"rd\"]=\"$res\"params[\"minband\"]=1params[\"nocc\"]=6params[\"maxband\"]=20params[\"nac_method\"]=0params[\"wfc_preprocess\"]=\"complete\"params[\"do_complete\"]=1params[\"prefix0\"]=\"x0.scf\"params[\"prefix1\"]=\"x1.scf\"params[\"compute_Hprime\"]=0print paramsrunMD1.runMD(params)"
cd $PBS_O_WORKDIRecho $PBS_O_WORKDIR
# Don't forget to source right MPI library:# source /usr/usc/openmpi/1.8.1/gnu/setup.shsource /home/export/parastor/clussoft/profile.d/intelmpi.sh
NP=$(wc -l $PBS_NODEFILE | awk '{print $1}') prefix = 'x0', outdir = './', pseudo_dir = '/home/export/parastor/keyuser/bnulongr/soft/qe/upf_files', psfile(1) = 'C.pbe-rrkjus.UPF', psfile(2) = 'H.pbe-rrkjus.UPF', single_file = .FALSE., ascii = .TRUE., uspp_spsi = .FALSE.,&CONTROL calculation = 'scf', pseudo_dir = '/home/export/parastor/keyuser/bnulongr/soft/qe/upf_files', outdir = './', prefix = 'x0', disk_io = 'low', wf_collect = .true./
&SYSTEM ibrav = 0, celldm(1) = 24.08, nat = 6, ntyp = 2, nspin = 2, nbnd = 20, ecutwfc = 30, tot_charge = 0.0, starting_magnetization(1) = 0.01 occupations = 'smearing', smearing = 'gaussian', degauss = 0.005, nosym = .true.,
/
&ELECTRONS electron_maxstep = 300, conv_thr = 1.D-5, mixing_beta = 0.45,/
&IONS ion_dynamics = 'verlet', ion_temperature = 'andersen', tempw = 300.00 , nraise = 1,/
ATOMIC_SPECIES C 12.01 C.pbe-rrkjus.UPF H 1.008 H.pbe-rrkjus.UPF
K_POINTS gamma CELL_PARAMETERS 1.0000000 0.0000000 0.0000000 0.0000000 1.0000000 0.0000000 0.0000000 0.0000000 1.0000000Best.
Misaraty
Alexey Akimov
Sep 9, 2017, 3:36:34 PM9/9/17
to Quantum-Dynamics-Hub
Hi Misaraty,
Would you give the Pyxaid2 a try? I haven't dealt with Pyxaid for a while, but remember that at some point they (QE) had wfc.1 files printed in a binary format. In which case I had an instruction to run a format conversion (via iotk module of QE). Later, it was not need to do this conversion so I removed the instruction. So, I'd recommend you looking inside the files (with vi) and determine if they are in binary or plane text format. In the latter case, it is likely that you have some other problems, more likely related to QE or parameters' setup. Just triple check everything.
Alexey
brendanqhd
Sep 9, 2017, 4:21:35 PM9/9/17
to Quantum-Dynamics-Hub
Hi Misaraty,
Is your problem that the files you need are not going into the res directory? If this is the case, you may want to make sure that you have properly placed the address of your res directory written correctly. Also, i see you have two different systems. One with just C and H, and the other with Pb and I in addition. Which exactly is it? the reason i am asking is because you may have forgotten a pseudo-potential for one of the atoms.
Best,
Brendan
Is your problem that the files you need are not going into the res directory? If this is the case, you may want to make sure that you have properly placed the address of your res directory written correctly. Also, i see you have two different systems. One with just C and H, and the other with Pb and I in addition. Which exactly is it? the reason i am asking is because you may have forgotten a pseudo-potential for one of the atoms.
Best,
Brendan
misa...@gmail.com
Sep 9, 2017, 10:19:02 PM9/9/17
to Quantum-Dynamics-Hub
Hi Brendan,
Thanks.
I used the two examples of calculation in the replies, one is provided by myself, the other is provided by the official. The pseudo-potential was suitable.
Best.
Misaraty
misa...@gmail.com
Sep 9, 2017, 10:25:33 PM9/9/17
to Quantum-Dynamics-Hub
Hi Alexey,
Thanks.
I checked wfc.1 file, which was a binary format file.
At present, pyxaid2 and parameters of QE are being tested.
Best.
Misaraty
Alexey Akimov
Sep 10, 2017, 5:55:09 AM9/10/17
to Quantum-Dynamics-Hub
Oh, ok. Then, you may want to try a different version of QE. Most of the QE versions produce these files in the xml format.
Alternatively, you would need a conversion like:
and then use the wfc.1.xml file instead of wfc.1 Well, it would be good to add this type of computational workflow, since the current assumption is that the files produced are already in a human-readable xml format.
os.system("%s convert %s/curr0/x0.export/wfc.1 %s/curr0/x0.export/wfc.1.xml" % (EXE_CONVERT,wd,wd))
Alexey
misa...@gmail.com
Sep 10, 2017, 5:58:52 AM9/10/17
to Quantum-Dynamics-Hub
Hi Alexey,
According to your instructions, I will have a try.
Best.
Misaraty
misa...@gmail.com
Sep 11, 2017, 10:25:11 AM9/11/17
to Quantum-Dynamics-Hub
Hi Alexey,
I test the pyxaid2 and have a question, why does ~/example/0-non-rel-non-sp/x0.scf.in file lack ATOMIC_POSITIONS parameter as official example of pyxaid/pyxaid2?
Thanks.
Best.
Misaraty
misa...@gmail.com
Sep 11, 2017, 10:56:49 AM9/11/17
to Quantum-Dynamics-Hub
Hi Alexey,
I add the details of the official example of pyxaid2 test and guess whether or not ATOMIC_POSITIONS parameter lacking is a problem.
path,
[bnulongr@sn21 0-non-rel-non-sp]$ pwd/home/export/parastor/keyuser/bnulongr/apps/test/test4/0-non-rel-non-sprun,
[bnulongr@sn21 0-non-rel-non-sp]$ python py-scr2.py /home/export/parastor/keyuser/bnulongr/apps/pyxaid2-master/PYXAID2/runMD.py:18: RuntimeWarning: to-Python converter for liblibra::libforcefield::Atom_Record already registered; second conversion method ignored. from liblibra_core import */home/export/parastor/keyuser/bnulongr/apps/pyxaid2-master/PYXAID2/runMD.py:18: RuntimeWarning: to-Python converter for std::vector<liblibra::libforcefield::Atom_Record, std::allocator<liblibra::libforcefield::Atom_Record> > already registered; second conversion method ignored. from liblibra_core import */home/export/parastor/keyuser/bnulongr/apps/pyxaid2-master/PYXAID2/runMD.py:18: RuntimeWarning: to-Python converter for boost::python::detail::container_element<std::vector<liblibra::libforcefield::Atom_Record, std::allocator<liblibra::libforcefield::Atom_Record> >, unsigned long, boost::python::detail::final_vector_derived_policies<std::vector<liblibra::libforcefield::Atom_Record, std::allocator<liblibra::libforcefield::Atom_Record> >, false> > already registered; second conversion method ignored. from liblibra_core import */home/export/parastor/keyuser/bnulongr/apps/pyxaid2-master/PYXAID2/runMD.py:18: RuntimeWarning: to-Python converter for liblibra::libforcefield::Bond_Record already registered; second conversion method ignored. from liblibra_core import */home/export/parastor/keyuser/bnulongr/apps/pyxaid2-master/PYXAID2/runMD.py:18: RuntimeWarning: to-Python converter for std::vector<liblibra::libforcefield::Bond_Record, std::allocator<liblibra::libforcefield::Bond_Record> > already registered; second conversion method ignored. from liblibra_core import */home/export/parastor/keyuser/bnulongr/apps/pyxaid2-master/PYXAID2/runMD.py:18: RuntimeWarning: to-Python converter for boost::python::detail::container_element<std::vector<liblibra::libforcefield::Bond_Record, std::allocator<liblibra::libforcefield::Bond_Record> >, unsigned long, boost::python::detail::final_vector_derived_policies<std::vector<liblibra::libforcefield::Bond_Record, std::allocator<liblibra::libforcefield::Bond_Record> >, false> > already registered; second conversion method ignored. from liblibra_core import */home/export/parastor/keyuser/bnulongr/apps/pyxaid2-master/PYXAID2/runMD.py:18: RuntimeWarning: to-Python converter for liblibra::libforcefield::Angle_Record already registered; second conversion method ignored. from liblibra_core import */home/export/parastor/keyuser/bnulongr/apps/pyxaid2-master/PYXAID2/runMD.py:18: RuntimeWarning: to-Python converter for std::vector<liblibra::libforcefield::Angle_Record, std::allocator<liblibra::libforcefield::Angle_Record> > already registered; second conversion method ignored. from liblibra_core import */home/export/parastor/keyuser/bnulongr/apps/pyxaid2-master/PYXAID2/runMD.py:18: RuntimeWarning: to-Python converter for boost::python::detail::container_element<std::vector<liblibra::libforcefield::Angle_Record, std::allocator<liblibra::libforcefield::Angle_Record> >, unsigned long, boost::python::detail::final_vector_derived_policies<std::vector<liblibra::libforcefield::Angle_Record, std::allocator<liblibra::libforcefield::Angle_Record> >, false> > already registered; second conversion method ignored. from liblibra_core import */home/export/parastor/keyuser/bnulongr/apps/pyxaid2-master/PYXAID2/runMD.py:18: RuntimeWarning: to-Python converter for liblibra::libforcefield::Dihedral_Record already registered; second conversion method ignored. from liblibra_core import */home/export/parastor/keyuser/bnulongr/apps/pyxaid2-master/PYXAID2/runMD.py:18: RuntimeWarning: to-Python converter for std::vector<liblibra::libforcefield::Dihedral_Record, std::allocator<liblibra::libforcefield::Dihedral_Record> > already registered; second conversion method ignored. from liblibra_core import */home/export/parastor/keyuser/bnulongr/apps/pyxaid2-master/PYXAID2/runMD.py:18: RuntimeWarning: to-Python converter for boost::python::detail::container_element<std::vector<liblibra::libforcefield::Dihedral_Record, std::allocator<liblibra::libforcefield::Dihedral_Record> >, unsigned long, boost::python::detail::final_vector_derived_policies<std::vector<liblibra::libforcefield::Dihedral_Record, std::allocator<liblibra::libforcefield::Dihedral_Record> >, false> > already registered; second conversion method ignored. from liblibra_core import */home/export/parastor/keyuser/bnulongr/apps/pyxaid2-master/PYXAID2/runMD.py:18: RuntimeWarning: to-Python converter for liblibra::libforcefield::Fragment_Record already registered; second conversion method ignored. from liblibra_core import */home/export/parastor/keyuser/bnulongr/apps/pyxaid2-master/PYXAID2/runMD.py:18: RuntimeWarning: to-Python converter for liblibra::libforcefield::ForceField already registered; second conversion method ignored. from liblibra_core import *39345.mgmt2.nsccjn.con39346.mgmt2.nsccjn.confiles distribution,
[bnulongr@sn21 0-non-rel-non-sp]$ tree.├── py-scr2.py├── py-scr3.py├── submit.pbs├── wd│ ├── job0│ │ ├── CRASH│ │ ├── qe_nac.o39345│ │ ├── submit.pbs│ │ ├── wd_test│ │ │ ├── curr0│ │ │ │ └── x0.scf.0.out│ │ │ └── next0│ │ │ └── x0.scf.1.out│ │ ├── x0.exp.in│ │ ├── x0.exp.out│ │ ├── x0.scf.0.in│ │ ├── x0.scf.1.in│ │ └── x0.scf.2.in│ ├── job1│ │ ├── CRASH│ │ ├── qe_nac.o39346│ │ ├── submit.pbs│ │ ├── wd_test│ │ │ ├── curr0│ │ │ │ └── x0.scf.2.out│ │ │ └── next0│ ├── submit.pbs│ ├── tmp│ ├── x0.exp.in│ ├── x0.scf.0.in│ ├── x0.scf.1.in│ ├── x0.scf.2.in│ ├── x0.scf.3.in│ └── x0.scf.4.in├── x0.exp.in└── x0.scf.in
9 directories, 32 fileserrors,
[bnulongr@sn21 0-non-rel-non-sp]$ nano /home/export/parastor/keyuser/bnulongr/apps/test/test4/0-non-rel-non-sp/wd/job0/CRASH
GNU nano 2.0.9 文件: ...test/test4/0-non-rel-non-sp/wd/job0/CRASH
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%$ task # 0 from pw_export : error # 1 reading inputpp namelist %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%$/home/export/parastor/keyuser/bnulongr/apps/test/test4/0-non-rel-non-sp/wd/job0/wd_test/curr0/x0.scf.0.out,
/home/export/parastor/keyuser/bnulongr/apps/test/test4/0-non-rel-non-sp/wd/job0/qe_nac.o39345,/home/export/parastor/keyuser/bnulongr/apps/test/test4/0-non-rel-non-sp/wd/job0/home/export/parastor/keyuser/bnulongr/apps/pyxaid2-master/PYXAID2/runMD.py:18: RuntimeWarning: to-Python converter for liblibra::libforcefield::Atom_Record already registered; second conversion method ignored. from liblibra_core import */home/export/parastor/keyuser/bnulongr/apps/pyxaid2-master/PYXAID2/runMD.py:18: RuntimeWarning: to-Python converter for std::vector<liblibra::libforcefield::Atom_Record, std::allocator<liblibra::libforcefield::Atom_Record> > already registered; second conversion method ignored. from liblibra_core import */home/export/parastor/keyuser/bnulongr/apps/pyxaid2-master/PYXAID2/runMD.py:18: RuntimeWarning: to-Python converter for boost::python::detail::container_element<std::vector<liblibra::libforcefield::Atom_Record, std::allocator<liblibra::libforcefield::Atom_Record> >, unsigned long, boost::python::detail::final_vector_derived_policies<std::vector<liblibra::libforcefield::Atom_Record, std::allocator<liblibra::libforcefield::Atom_Record> >, false> > already registered; second conversion method ignored. from liblibra_core import */home/export/parastor/keyuser/bnulongr/apps/pyxaid2-master/PYXAID2/runMD.py:18: RuntimeWarning: to-Python converter for liblibra::libforcefield::Bond_Record already registered; second conversion method ignored. from liblibra_core import */home/export/parastor/keyuser/bnulongr/apps/pyxaid2-master/PYXAID2/runMD.py:18: RuntimeWarning: to-Python converter for std::vector<liblibra::libforcefield::Bond_Record, std::allocator<liblibra::libforcefield::Bond_Record> > already registered; second conversion method ignored. from liblibra_core import */home/export/parastor/keyuser/bnulongr/apps/pyxaid2-master/PYXAID2/runMD.py:18: RuntimeWarning: to-Python converter for boost::python::detail::container_element<std::vector<liblibra::libforcefield::Bond_Record, std::allocator<liblibra::libforcefield::Bond_Record> >, unsigned long, boost::python::detail::final_vector_derived_policies<std::vector<liblibra::libforcefield::Bond_Record, std::allocator<liblibra::libforcefield::Bond_Record> >, false> > already registered; second conversion method ignored. from liblibra_core import */home/export/parastor/keyuser/bnulongr/apps/pyxaid2-master/PYXAID2/runMD.py:18: RuntimeWarning: to-Python converter for liblibra::libforcefield::Angle_Record already registered; second conversion method ignored. from liblibra_core import */home/export/parastor/keyuser/bnulongr/apps/pyxaid2-master/PYXAID2/runMD.py:18: RuntimeWarning: to-Python converter for std::vector<liblibra::libforcefield::Angle_Record, std::allocator<liblibra::libforcefield::Angle_Record> > already registered; second conversion method ignored. from liblibra_core import */home/export/parastor/keyuser/bnulongr/apps/pyxaid2-master/PYXAID2/runMD.py:18: RuntimeWarning: to-Python converter for boost::python::detail::container_element<std::vector<liblibra::libforcefield::Angle_Record, std::allocator<liblibra::libforcefield::Angle_Record> >, unsigned long, boost::python::detail::final_vector_derived_policies<std::vector<liblibra::libforcefield::Angle_Record, std::allocator<liblibra::libforcefield::Angle_Record> >, false> > already registered; second conversion method ignored. from liblibra_core import */home/export/parastor/keyuser/bnulongr/apps/pyxaid2-master/PYXAID2/runMD.py:18: RuntimeWarning: to-Python converter for liblibra::libforcefield::Dihedral_Record already registered; second conversion method ignored. from liblibra_core import */home/export/parastor/keyuser/bnulongr/apps/pyxaid2-master/PYXAID2/runMD.py:18: RuntimeWarning: to-Python converter for std::vector<liblibra::libforcefield::Dihedral_Record, std::allocator<liblibra::libforcefield::Dihedral_Record> > already registered; second conversion method ignored. from liblibra_core import */home/export/parastor/keyuser/bnulongr/apps/pyxaid2-master/PYXAID2/runMD.py:18: RuntimeWarning: to-Python converter for boost::python::detail::container_element<std::vector<liblibra::libforcefield::Dihedral_Record, std::allocator<liblibra::libforcefield::Dihedral_Record> >, unsigned long, boost::python::detail::final_vector_derived_policies<std::vector<liblibra::libforcefield::Dihedral_Record, std::allocator<liblibra::libforcefield::Dihedral_Record> >, false> > already registered; second conversion method ignored. from liblibra_core import */home/export/parastor/keyuser/bnulongr/apps/pyxaid2-master/PYXAID2/runMD.py:18: RuntimeWarning: to-Python converter for liblibra::libforcefield::Fragment_Record already registered; second conversion method ignored. from liblibra_core import */home/export/parastor/keyuser/bnulongr/apps/pyxaid2-master/PYXAID2/runMD.py:18: RuntimeWarning: to-Python converter for liblibra::libforcefield::ForceField already registered; second conversion method ignored. from liblibra_core import */home/export/parastor/keyuser/bnulongr/apps/test/test4/0-non-rel-non-sp/wd/job0application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0mv: cannot stat `*.wfc*': No such file or directorymv: cannot stat `x0.export': No such file or directoryapplication called MPI_Abort(MPI_COMM_WORLD, 1) - process 0application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0mv: cannot stat `*.wfc*': No such file or directorymv: cannot stat `x0.export': No such file or directory{'maxband_soc': 37, 'maxband': 37, 'EXE': '/home/export/parastor/keyuser/bnulongr/apps/qe/5.3.0/espresso-5.3.0/bin/pw.x', 'wd': 'wd_test', 'compute_Hprime': 0, 'BATCH_SYSTEM': '/home/export/parastor/clussoft/mpi/openmpi/1.8.7/intel/bin/mpirun', 'prefix1': 'x1.scf', 'prefix0': 'x0.scf', 'minband': 36, 'stop_indx': 2, 'rd': '/home/export/parastor/keyuser/bnulongr/apps/test/test4/0-non-rel-non-sp/res', 'start_indx': 0, 'pptype': 'US', 'EXE_EXPORT': '/home/export/parastor/keyuser/bnulongr/apps/qe/5.3.0/espresso-5.3.0/bin/pw_export.x', 'nac_method': 0, 'wfc_preprocess': 'complete', 'do_complete': 1, 'NP': 1, 'EXE_CONVERT': '/home/export/parastor/keyuser/bnulongr/apps/qe/5.3.0/espresso-5.3.0/bin/iotk', 'minband_soc': 36}Starting runMDWarning: Parameter with key = dt does not exist in dictionaryUsing the default value of 1.0Warning: Parameter with key = pp_type does not exist in dictionaryUsing the default value of NCnon-relativistic, non spin-polarized calculation for NAC
In runMD: current working directory for python: /home/export/parastor/keyuser/bnulongr/apps/test/test4/0-non-rel-non-sp/wd/job0In runMD: current working directory for sh: 0>>>>>>>>>>>>>>>>>>>> t= 0 <<<<<<<<<<<<<<<<<<<<<Starting first point in this batchTime to run first calculations = 0.01End of step t= 0>>>>>>>>>>>>>>>>>>>> t= 1 <<<<<<<<<<<<<<<<<<<<<Continuing with other points in this batchTime to run first calculations = 0.01Generate NAC from WFCs at two adjacent pointsTraceback (most recent call last): File "<string>", line 24, in <module> File "/home/export/parastor/keyuser/bnulongr/apps/pyxaid2-master/PYXAID2/runMD2.py", line 562, in runMD info0, all_e_dum0 = QE_methods.read_qe_index("%s/curr0/x0.export/index.xml" % wd, [], 0) File "/home/export/parastor/keyuser/bnulongr/apps/libra/bin/src/libra_py/QE_methods.py", line 41, in read_qe_index ctx = Context(filename) #("x.export/index.xml")RuntimeError: wd_test/curr0/x0.export/index.xml: cannot open file-----------------------------------------------------------------------------------------
input files,
py-scr2.py,
from PYXAID2 import *import os
user = 1 #weili or eric#user = 2 #alexey
nsteps_per_job = 2tot_nsteps = 4
# Step 1 - split MD trajectory on the time steps# IMPORTANT: # 1) use only ABSOLUTE path for PP in x.scf.in file# 2) provided input file is just a template, so do not include coordinates
# Step 2 - distribute all time steps into groups(jobs) # several time steps per group - this is to accelerate calculations# creates a "customized" submit file for each job and submit it - run# a swarm in independent calculations (trajectory pieces)#(HTC paradigm)# Provide the files below: # submit_templ.pbs - template for submit files - manually edit the variables# x.exp.in - file for export of the wavefunction
if user==1: os.system("cp submit.pbs wd")elif user==2: os.system("cp submit_templ.slm wd")if user==1: #distribute.distribute(0,tot_nsteps,nsteps_per_job,"submit.pbs",["x0.exp.in","x1.exp.in"],["x0.scf","x1.scf"],1) distribute.distribute(0,tot_nsteps,nsteps_per_job,"submit.pbs",["x0.exp.in"],["x0.scf"],1) #distribute.distribute(0,tot_nsteps,nsteps_per_job,"submit.pbs",["x1.exp.in"],["x1.scf"],1)# elif user==2: #distribute.distribute(0,tot_nsteps,nsteps_per_job,"submit_templ.slm",["x0.exp.in"],["x0.scf"],2) #distribute.distribute(0,tot_nsteps,nsteps_per_job,"submit_templ.slm",["x1.exp.in"],["x1.scf"],2)submit.pbs,
#!/bin/bash#PBS -l nodes=1:ppn=1#PBS -N qe_nac#PBS -j oe#PBS -q q_zhq_bnulongr#PBS -l walltime=30:00:00
cd $PBS_O_WORKDIRecho $PBS_O_WORKDIR
# the below settings works for my laptop, please customize your own environmental variables!###### some conventional settings ############ export PYTHONPATH=/home/eric/src/Libra/libra-code/_build/src:$PYTHONPATH# export LD_LIBRARY_PATH=/home/eric/src/Libra/libra-code/_build/src:$LD_LIBRARY_PATH# export PYTHONPATH=/home/eric/src/Libra/pyxaid2:$PYTHONPATH# export LD_LIBRARY_PATH=/home/eric/src/Libra/pyxaid2:/opt/boost/1.55.0/lib:$LD_LIBRARY_PATH# export LD_LIBRARY_PATH=/opt/intel/composer_xe_2013.1.117/mkl/lib/intel64:$LD_LIBRARY_PATHexport PYTHONPATH=/home/export/parastor/keyuser/bnulongr/apps/libra/bin/src:$PYTHONPATHexport LD_LIBRARY_PATH=/home/export/parastor/keyuser/bnulongr/apps/libra/bin/src:$LD_LIBRARY_PATHexport PYTHONPATH=/home/export/parastor/keyuser/bnulongr/apps/pyxaid2-master:$PYTHONPATHexport LD_LIBRARY_PATH=/home/export/parastor/keyuser/bnulongr/apps/pyxaid2-master:/home/export/parastor/keyuser/bnulongr/apps/boost1.6/lib:$LD_LIBRARY_PATHexport LD_LIBRARY_PATH=/home/export/parastor/clussoft/compiler/intel/composer_xe_2015.2.164/mkl/lib/intel64:$LD_LIBRARY_PATH##### path for the QE module #####exe_qespresso=/home/export/parastor/keyuser/bnulongr/apps/qe/5.3.0/espresso-5.3.0/bin/pw.xexe_export=/home/export/parastor/keyuser/bnulongr/apps/qe/5.3.0/espresso-5.3.0/bin/pw_export.xexe_convert=/home/export/parastor/keyuser/bnulongr/apps/qe/5.3.0/espresso-5.3.0/bin/iotk##### MPI #####MPIRUN=/home/export/parastor/clussoft/mpi/openmpi/1.8.7/intel/bin/mpirunNP=$(wc -l $PBS_NODEFILE | awk '{print $1}')
# These will be assigned automatically, leave them as they areparam1=param2=
res=/home/export/parastor/keyuser/bnulongr/apps/test/test4/0-non-rel-non-sp/res
# This is invocation of the scripts which will further handle NA-MD calclculations# on the NAC calculation steppython -c "from PYXAID2 import *params = { }params[\"BATCH_SYSTEM\"]=\"$MPIRUN\"params[\"NP\"]=$NPparams[\"EXE\"]=\"$exe_qespresso\"params[\"EXE_EXPORT\"]=\"$exe_export\"params[\"EXE_CONVERT\"] =\"$exe_convert\"params[\"start_indx\"]=$param1params[\"stop_indx\"]=$param2params[\"wd\"]=\"wd_test\"params[\"rd\"]=\"$res\"params[\"minband\"]=36params[\"maxband\"]=37params[\"minband_soc\"]=36params[\"maxband_soc\"]=37params[\"nac_method\"]=0params[\"wfc_preprocess\"]=\"complete\"params[\"do_complete\"]=1params[\"prefix0\"]=\"x0.scf\"params[\"prefix1\"]=\"x1.scf\"params[\"compute_Hprime\"]=0params[\"pptype\"]=\"US\"print params&inputpp prefix = 'x0', outdir = './', pseudo_dir = '/home/export/parastor/keyuser/bnulongr/apps/test/test4/pp', psfile(1) = 'Ga.pbe-dn-rrkjus_psl.0.2.UPF', psfile(2) = 'As.pbe-n-rrkjus_psl.0.2.UPF', single_file = .FALSE., ascii = .TRUE., uspp_spsi = .FALSE.,/&CONTROL calculation = 'scf', dt = 20.67055,! nstep = 50, pseudo_dir = '/home/export/parastor/keyuser/bnulongr/apps/test/test4/pp', outdir = './', prefix = 'x0', disk_io = 'low', wf_collect = .true./&SYSTEM ibrav = 0, celldm(1) = 1.89, nat = 8, ntyp = 2,! nspin = 2, nbnd = 50, ecutwfc = 50, tot_charge = 0.0, occupations = 'smearing',! starting_magnetization(1) = 0.01, smearing = 'gaussian', degauss = 0.005, nosym = .true., !lspinorb=.true., !noncolin = .true.,/&ELECTRONS electron_maxstep = 300, conv_thr = 1.D-5, mixing_beta = 0.45,/&IONS ion_dynamics = 'verlet', ion_temperature = 'andersen', tempw = 300.00 , nraise = 1,/ATOMIC_SPECIES Ga 69.723 Ga.pbe-dn-rrkjus_psl.0.2.UPF As 74.921 As.pbe-n-rrkjus_psl.0.2.UPFK_POINTS automatic1 1 1 0 0 0 CELL_PARAMETERS 5.745328496 0.000000000 0.000000000 0.000000000 5.745329803 0.000000000 0.000000000 0.000000000 5.745329473 Best.
Misaraty
Wei Li
Sep 11, 2017, 11:40:17 AM9/11/17
to Quantum-Dynamics-Hub
Hi Misaraty,
The error reminds "reading inputpp namelist", it may come from the error namelist in the QE input file, maybe you should check it carefully.
Wei
misa...@gmail.com
Sep 11, 2017, 9:12:11 PM9/11/17
to Quantum-Dynamics-Hub
Hi Wei,
Thanks.
I used the official example of pyxaid2 (pyxaid was also a similar situation), just modified the path of pseudo_dir parameter.
But I did not know why the *.in, which was QE input file, did not contain the ATOMIC_POSITIONS parameter?
Best.
Misaraty
Alexey Akimov
Sep 12, 2017, 1:15:13 AM9/12/17
to Quantum-Dynamics-Hub
Hi Misaraty,
Have you looked at the Pyxaid (1!) tutorials? As far as I remember, there is an explanation for why there is not ATOMIC_POSITIONS parameters in that file.
Alexey
brendanqhd
Sep 13, 2017, 1:29:31 PM9/13/17
to Quantum-Dynamics-Hub
Hi Misaraty,
The atomic positions are not included in step 2 of PYXAID because you actually already computer the atomic positions at each time step during step 1 of PYXAID. You have to make sure that the x.md.out file from step 1 is in the step 2 directory. Have you done this already? I am trying to gauge where you are.
Best,
Brendan
misa...@gmail.com
Sep 13, 2017, 8:32:56 PM9/13/17
to Quantum-Dynamics-Hub
Hi Brendan,
Thanks.
Yes. The x.md.out file from step 1 is really in the step 2 directory.
Best.
Misaraty
misa...@gmail.com
Sep 17, 2017, 10:15:34 AM9/17/17
to Quantum-Dynamics-Hub
Hi Alexey,
The pyxiad2+qe is already running. Thanks for you, Wei and Brendan.
Best.
Misaraty
brendanqhd
Sep 17, 2017, 4:34:14 PM9/17/17
to Quantum-Dynamics-Hub
Hi, Misaraty,
So is everything working fine? If not -- what specifically is not working, I am still not completely following what the specific problem is you are having. Could you try to say it in 2-3 sentences?
Best,
Brendan
So is everything working fine? If not -- what specifically is not working, I am still not completely following what the specific problem is you are having. Could you try to say it in 2-3 sentences?
Best,
Brendan
misa...@gmail.com
Sep 17, 2017, 11:10:13 PM9/17/17
to Quantum-Dynamics-Hub
Hi Brendan,
Thanks.
Yes. At present, it is normal.
The main problem is the mpi parameters of QE installation need to be modified. I installed the software on multiple clusters. Since the cluster environment is different, the same installation steps do not seem to guarantee the same result, even if you have installed all the dependencies alone.
Best.
Misaraty
brendanqhd
Sep 18, 2017, 11:05:45 AM9/18/17
to Quantum-Dynamics-Hub
Great, Glad to hear it is working,
Best,
Brendan
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