From ddb871bafaa02a0fabc96bb31d305161636c743e Mon Sep 17 00:00:00 2001 From: cpolanco Date: Wed, 7 Dec 2022 00:48:07 +0100 Subject: [PATCH 1/3] Did the initial structe of the code. Create a class to handle QE input files. Create functions to read the input and create other inputs base on the class. For the moment this only works for kgrid. --- capolanco/README.md | 37 ++ capolanco/RunConvergence.py | 53 +++ capolanco/Si.scf.in | 30 ++ capolanco/Si.scf.out | 437 ++++++++++++++++++ .../__pycache__/ioqeclass.cpython-39.pyc | Bin 0 -> 1529 bytes capolanco/ioqeclass.py | 90 ++++ capolanco/test.scf.in | 30 ++ capolanco/test.scf.out | 437 ++++++++++++++++++ 8 files changed, 1114 insertions(+) create mode 100644 capolanco/README.md create mode 100644 capolanco/RunConvergence.py create mode 100644 capolanco/Si.scf.in create mode 100644 capolanco/Si.scf.out create mode 100644 capolanco/__pycache__/ioqeclass.cpython-39.pyc create mode 100644 capolanco/ioqeclass.py create mode 100644 capolanco/test.scf.in create mode 100644 capolanco/test.scf.out diff --git a/capolanco/README.md b/capolanco/README.md new file mode 100644 index 00000000..cbd01009 --- /dev/null +++ b/capolanco/README.md @@ -0,0 +1,37 @@ +# K-point convergence tracker (Materials) + +> Ideal candidate: scientists skilled in Density Functional Theory and proficient in python. + +# Overview + +The aim of this task is to create a python package that implements automatic convergence tracking mechanism for a materials simulations engine. The convergence is tracked with respect to the k-point sampling inside a reciprocal cell of a crystalline compound. + +# Requirements + +1. automatically find the dimensions of a k-point mesh that satisfy a certain criteria for total energy (eg. total energy is converged within dE = 0.01meV) +1. the code shall be written in a way that can facilitate easy addition of convergence wrt other characteristics extracted from simulations (forces, pressures, phonon frequencies etc) +1. the code shall support VASP or Quantum ESPRESSO + +# Expectations + +- correctly find k-point mesh that satisfies total energy convergence parameters for a set of 10 materials, starting from Si2, as simplest, to a 10-20-atom supercell of your choice +- modular and object-oriented implementation +- commit early and often - at least once per 24 hours + +# Timeline + +We leave exact timing to the candidate. Must fit Within 5 days total. + +# User story + +As a user of this software I can start it passing: + +- path to input data (eg. pw.in / POSCAR, INCAR, KPOINTS) and +- kinetic energy cutoff + +as parameters and get the k-point dimensions (eg. 5 5 5). + +# Notes + +- create an account at exabyte.io and use it for the calculation purposes +- suggested modeling engine: Quantum ESPRESSO diff --git a/capolanco/RunConvergence.py b/capolanco/RunConvergence.py new file mode 100644 index 00000000..f9256a09 --- /dev/null +++ b/capolanco/RunConvergence.py @@ -0,0 +1,53 @@ +# This code will run a k-point convergence up to a desire delta energy + + +import ioqeclass as qe + +########################### +##### USER INPUTS +########################### + +# Define the path of the input file +# The k-grid of this file will be set as the starting point +# for the convergence process +filein='Si.scf.in' + +# Define delta energy threshold for +# convergence (eV) +dE=1 # (eV) + + + +########################### +##### PROGRAM +########################### + + +### Set up initial parameters +# Initialize pw.x input class +qeinput=qe.qepwinput() +# load the pw.x input +qeinput.load(filein) +# Create the input file for initial run +testin='test.scf.in' +testout='test.scf.out' +qeinput.save(filein,testin) +# Run initial test +##### pw.x test.scf.in test.scf.out +# Read the Total energy from the output + + +# Loop testing for dE + +## set up calculation +#fileout='test.scf.in' +#qeinput.save(filein,fileout) + +## run pw.x + +## extract the total energy + +## compare with the threshold + + + diff --git a/capolanco/Si.scf.in b/capolanco/Si.scf.in new file mode 100644 index 00000000..0bd51ddd --- /dev/null +++ b/capolanco/Si.scf.in @@ -0,0 +1,30 @@ + &control + calculation='scf', + outdir = '/global/cscratch1/sd/cpolanco/Si/', + prefix='Si', + pseudo_dir = '/global/homes/c/cpolanco/Materials/pseudo/', + restart_mode='from_scratch', + tprnfor= .true., + tstress= .true., + / + &system + ibrav= 2, + celldm(1)= 10.20777693, + nat= 2, + ntyp= 1, + ecutwfc= 100.0 + / + &electrons + mixing_beta= 0.7 + conv_thr= 1.0d-14 + / + +ATOMIC_SPECIES + Si 28.086 Si.pz-vbc.UPF + +ATOMIC_POSITIONS (alat) + Si 0.00 0.00 0.00 + Si 0.25 0.25 0.25 + +K_POINTS (automatic) + 8 8 8 0 0 0 diff --git a/capolanco/Si.scf.out b/capolanco/Si.scf.out new file mode 100644 index 00000000..ce3f6334 --- /dev/null +++ b/capolanco/Si.scf.out @@ -0,0 +1,437 @@ + + Program PWSCF v.6.1 starts on 27Sep2017 at 19:30: 1 + + 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); + 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 & OpenMP), running on 24 processor cores + Number of MPI processes: 24 + Threads/MPI process: 1 + R & G space division: proc/nbgrp/npool/nimage = 24 + Waiting for input... + Reading input from standard input + + 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 + + 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 59 59 17 1489 1489 232 + Max 60 60 18 1494 1494 235 + Sum 1417 1417 421 35749 35749 5601 + + + + bravais-lattice index = 2 + lattice parameter (alat) = 10.2078 a.u. + unit-cell volume = 265.9093 (a.u.)^3 + number of atoms/cell = 2 + number of atomic types = 1 + number of electrons = 8.00 + number of Kohn-Sham states= 4 + kinetic-energy cutoff = 100.0000 Ry + charge density cutoff = 400.0000 Ry + convergence threshold = 1.0E-14 + mixing beta = 0.7000 + number of iterations used = 8 plain mixing + Exchange-correlation = SLA PZ NOGX NOGC ( 1 1 0 0 0 0) + + celldm(1)= 10.207777 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) = ( -0.500000 0.000000 0.500000 ) + a(2) = ( 0.000000 0.500000 0.500000 ) + a(3) = ( -0.500000 0.500000 0.000000 ) + + reciprocal axes: (cart. coord. in units 2 pi/alat) + b(1) = ( -1.000000 -1.000000 1.000000 ) + b(2) = ( 1.000000 1.000000 1.000000 ) + b(3) = ( -1.000000 1.000000 -1.000000 ) + + + PseudoPot. # 1 for Si read from file: + /global/homes/c/cpolanco/Materials/pseudo/Si.pz-vbc.UPF + MD5 check sum: 6dfa03ddd5817404712e03e4d12deb78 + Pseudo is Norm-conserving, Zval = 4.0 + Generated by new atomic code, or converted to UPF format + Using radial grid of 431 points, 2 beta functions with: + l(1) = 0 + l(2) = 1 + + atomic species valence mass pseudopotential + Si 4.00 28.08600 Si( 1.00) + + 24 Sym. Ops. (no inversion) found + (note: 24 additional sym.ops. were found but ignored + their fractional translations are incommensurate with FFT grid) + + + Cartesian axes + + site n. atom positions (alat units) + 1 Si tau( 1) = ( 0.0000000 0.0000000 0.0000000 ) + 2 Si tau( 2) = ( 0.2500000 0.2500000 0.2500000 ) + + number of k points= 29 + cart. coord. in units 2pi/alat + k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 0.0039062 + k( 2) = ( -0.1250000 0.1250000 -0.1250000), wk = 0.0312500 + k( 3) = ( -0.2500000 0.2500000 -0.2500000), wk = 0.0312500 + k( 4) = ( -0.3750000 0.3750000 -0.3750000), wk = 0.0312500 + k( 5) = ( 0.5000000 -0.5000000 0.5000000), wk = 0.0156250 + k( 6) = ( 0.0000000 0.2500000 0.0000000), wk = 0.0234375 + k( 7) = ( -0.1250000 0.3750000 -0.1250000), wk = 0.0937500 + k( 8) = ( -0.2500000 0.5000000 -0.2500000), wk = 0.0937500 + k( 9) = ( 0.6250000 -0.3750000 0.6250000), wk = 0.0937500 + k( 10) = ( 0.5000000 -0.2500000 0.5000000), wk = 0.0937500 + k( 11) = ( 0.3750000 -0.1250000 0.3750000), wk = 0.0937500 + k( 12) = ( 0.2500000 0.0000000 0.2500000), wk = 0.0468750 + k( 13) = ( 0.0000000 0.5000000 0.0000000), wk = 0.0234375 + k( 14) = ( -0.1250000 0.6250000 -0.1250000), wk = 0.0937500 + k( 15) = ( 0.7500000 -0.2500000 0.7500000), wk = 0.0937500 + k( 16) = ( 0.6250000 -0.1250000 0.6250000), wk = 0.0937500 + k( 17) = ( 0.5000000 0.0000000 0.5000000), wk = 0.0468750 + k( 18) = ( 0.0000000 0.7500000 0.0000000), wk = 0.0234375 + k( 19) = ( 0.8750000 -0.1250000 0.8750000), wk = 0.0937500 + k( 20) = ( 0.7500000 0.0000000 0.7500000), wk = 0.0468750 + k( 21) = ( 0.0000000 -1.0000000 0.0000000), wk = 0.0117188 + k( 22) = ( -0.2500000 0.5000000 0.0000000), wk = 0.0937500 + k( 23) = ( 0.6250000 -0.3750000 0.8750000), wk = 0.1875000 + k( 24) = ( 0.5000000 -0.2500000 0.7500000), wk = 0.0937500 + k( 25) = ( 0.7500000 -0.2500000 1.0000000), wk = 0.0937500 + k( 26) = ( 0.6250000 -0.1250000 0.8750000), wk = 0.1875000 + k( 27) = ( 0.5000000 0.0000000 0.7500000), wk = 0.0937500 + k( 28) = ( -0.2500000 -1.0000000 0.0000000), wk = 0.0468750 + k( 29) = ( -0.5000000 -1.0000000 0.0000000), wk = 0.0234375 + + Dense grid: 35749 G-vectors FFT dimensions: ( 45, 45, 45) + + Estimated max dynamical RAM per process > 1.29MB + + Estimated total allocated dynamical RAM > 31.06MB + + Initial potential from superposition of free atoms + + starting charge 7.99901, renormalised to 8.00000 + Starting wfc are 8 randomized atomic wfcs + + total cpu time spent up to now is 0.4 secs + + per-process dynamical memory: 2.9 Mb + + Self-consistent Calculation + + iteration # 1 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.00E-02, avg # of iterations = 2.0 + + Threshold (ethr) on eigenvalues was too large: + Diagonalizing with lowered threshold + + Davidson diagonalization with overlap + ethr = 7.97E-04, avg # of iterations = 1.0 + + total cpu time spent up to now is 0.6 secs + + total energy = -15.84982619 Ry + Harris-Foulkes estimate = -15.87079416 Ry + estimated scf accuracy < 0.06161703 Ry + + iteration # 2 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 7.70E-04, avg # of iterations = 1.0 + + total cpu time spent up to now is 0.7 secs + + total energy = -15.85288351 Ry + Harris-Foulkes estimate = -15.85318795 Ry + estimated scf accuracy < 0.00216687 Ry + + iteration # 3 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 2.71E-05, avg # of iterations = 2.4 + + total cpu time spent up to now is 0.8 secs + + total energy = -15.85332918 Ry + Harris-Foulkes estimate = -15.85336185 Ry + estimated scf accuracy < 0.00007437 Ry + + iteration # 4 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 9.30E-07, avg # of iterations = 2.1 + + total cpu time spent up to now is 0.8 secs + + total energy = -15.85334986 Ry + Harris-Foulkes estimate = -15.85335396 Ry + estimated scf accuracy < 0.00000888 Ry + + iteration # 5 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.11E-07, avg # of iterations = 2.1 + + total cpu time spent up to now is 0.9 secs + + total energy = -15.85335134 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 0.00000011 Ry + + iteration # 6 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.35E-09, avg # of iterations = 2.6 + + total cpu time spent up to now is 1.0 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 2.9E-09 Ry + + iteration # 7 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 3.68E-11, avg # of iterations = 2.6 + + total cpu time spent up to now is 1.1 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 2.9E-11 Ry + + iteration # 8 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 3.65E-13, avg # of iterations = 3.3 + + total cpu time spent up to now is 1.2 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 5.4E-12 Ry + + iteration # 9 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.00E-13, avg # of iterations = 1.7 + + total cpu time spent up to now is 1.3 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 1.2E-13 Ry + + iteration # 10 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.00E-13, avg # of iterations = 1.0 + + total cpu time spent up to now is 1.4 secs + + End of self-consistent calculation + + k = 0.0000 0.0000 0.0000 ( 4477 PWs) bands (ev): + + -5.8300 6.2061 6.2061 6.2061 + + k =-0.1250 0.1250-0.1250 ( 4507 PWs) bands (ev): + + -5.6230 4.6051 5.9132 5.9132 + + k =-0.2500 0.2500-0.2500 ( 4510 PWs) bands (ev): + + -5.0182 2.2559 5.4373 5.4373 + + k =-0.3750 0.3750-0.3750 ( 4501 PWs) bands (ev): + + -4.1058 0.2065 5.1074 5.1074 + + k = 0.5000-0.5000 0.5000 ( 4476 PWs) bands (ev): + + -3.4453 -0.8427 4.9947 4.9947 + + k = 0.0000 0.2500 0.0000 ( 4504 PWs) bands (ev): + + -5.5533 4.8935 5.3857 5.3857 + + k =-0.1250 0.3750-0.1250 ( 4517 PWs) bands (ev): + + -5.0777 2.9801 4.8669 4.9518 + + k =-0.2500 0.5000-0.2500 ( 4508 PWs) bands (ev): + + -4.2481 0.8896 4.3532 4.5964 + + k = 0.6250-0.3750 0.6250 ( 4486 PWs) bands (ev): + + -3.3613 -0.6068 3.9003 4.6231 + + k = 0.5000-0.2500 0.5000 ( 4491 PWs) bands (ev): + + -3.6148 -0.2257 3.7125 4.9256 + + k = 0.3750-0.1250 0.3750 ( 4497 PWs) bands (ev): + + -4.5602 1.5598 3.8591 5.4251 + + k = 0.2500 0.0000 0.2500 ( 4477 PWs) bands (ev): + + -5.2819 3.5267 4.5444 5.9125 + + k = 0.0000 0.5000 0.0000 ( 4520 PWs) bands (ev): + + -4.7329 2.7148 4.2862 4.2862 + + k =-0.1250 0.6250-0.1250 ( 4509 PWs) bands (ev): + + -4.0117 1.2745 3.4881 3.9636 + + k = 0.7500-0.2500 0.7500 ( 4482 PWs) bands (ev): + + -3.0647 -0.1975 2.6082 3.9678 + + k = 0.6250-0.1250 0.6250 ( 4477 PWs) bands (ev): + + -2.8512 -0.4657 2.1376 4.2926 + + k = 0.5000 0.0000 0.5000 ( 4489 PWs) bands (ev): + + -3.7521 0.7207 2.3750 4.8614 + + k = 0.0000 0.7500 0.0000 ( 4484 PWs) bands (ev): + + -3.4015 0.4708 3.5586 3.5586 + + k = 0.8750-0.1250 0.8750 ( 4479 PWs) bands (ev): + + -2.4888 -0.6253 2.7002 3.4815 + + k = 0.7500 0.0000 0.7500 ( 4454 PWs) bands (ev): + + -2.0305 -1.0339 1.8049 3.7440 + + k = 0.0000-1.0000 0.0000 ( 4456 PWs) bands (ev): + + -1.6267 -1.6267 3.3090 3.3090 + + k =-0.2500 0.5000 0.0000 ( 4503 PWs) bands (ev): + + -4.4807 1.9234 3.4393 4.7592 + + k = 0.6250-0.3750 0.8750 ( 4489 PWs) bands (ev): + + -3.5748 0.3447 2.8290 4.2439 + + k = 0.5000-0.2500 0.7500 ( 4486 PWs) bands (ev): + + -2.9014 -0.6278 2.7039 4.0076 + + k = 0.7500-0.2500 1.0000 ( 4484 PWs) bands (ev): + + -3.1970 0.2501 2.7770 3.3923 + + k = 0.6250-0.1250 0.8750 ( 4486 PWs) bands (ev): + + -2.3006 -0.7332 2.0576 3.1860 + + k = 0.5000 0.0000 0.7500 ( 4490 PWs) bands (ev): + + -2.6570 -0.3670 1.8851 3.5717 + + k =-0.2500-1.0000 0.0000 ( 4472 PWs) bands (ev): + + -1.5427 -1.5427 2.7194 2.7194 + + k =-0.5000-1.0000 0.0000 ( 4488 PWs) bands (ev): + + -1.4495 -1.4495 2.2655 2.2655 + + highest occupied level (ev): 6.2061 + +! total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 4.0E-15 Ry + + The total energy is the sum of the following terms: + + one-electron contribution = 4.76680131 Ry + hartree contribution = 1.08149972 Ry + xc contribution = -4.81476914 Ry + ewald contribution = -16.88688327 Ry + + convergence has been achieved in 10 iterations + + Forces acting on atoms (cartesian axes, Ry/au): + + atom 1 type 1 force = 0.00000000 0.00000000 0.00000000 + atom 2 type 1 force = 0.00000000 0.00000000 -0.00000000 + + Total force = 0.000000 Total SCF correction = 0.000000 + + + Computing stress (Cartesian axis) and pressure + + total stress (Ry/bohr**3) (kbar) P= 0.05 + 0.00000032 -0.00000000 -0.00000000 0.05 -0.00 -0.00 + -0.00000000 0.00000032 0.00000000 -0.00 0.05 0.00 + -0.00000000 0.00000000 0.00000032 -0.00 0.00 0.05 + + + Writing output data file Si.save + + init_run : 0.06s CPU 0.23s WALL ( 1 calls) + electrons : 0.85s CPU 1.01s WALL ( 1 calls) + forces : 0.00s CPU 0.01s WALL ( 1 calls) + stress : 0.02s CPU 0.03s WALL ( 1 calls) + + Called by init_run: + wfcinit : 0.04s CPU 0.11s WALL ( 1 calls) + potinit : 0.00s CPU 0.01s WALL ( 1 calls) + + Called by electrons: + c_bands : 0.73s CPU 0.80s WALL ( 11 calls) + sum_band : 0.11s CPU 0.13s WALL ( 11 calls) + v_of_rho : 0.00s CPU 0.01s WALL ( 11 calls) + mix_rho : 0.00s CPU 0.01s WALL ( 11 calls) + + Called by c_bands: + init_us_2 : 0.01s CPU 0.03s WALL ( 725 calls) + cegterg : 0.69s CPU 0.74s WALL ( 319 calls) + + Called by sum_band: + + Called by *egterg: + h_psi : 0.62s CPU 0.65s WALL ( 980 calls) + g_psi : 0.00s CPU 0.00s WALL ( 632 calls) + cdiaghg : 0.05s CPU 0.10s WALL ( 922 calls) + + Called by h_psi: + h_psi:pot : 0.61s CPU 0.65s WALL ( 980 calls) + h_psi:calbec : 0.03s CPU 0.04s WALL ( 980 calls) + vloc_psi : 0.57s CPU 0.59s WALL ( 980 calls) + add_vuspsi : 0.01s CPU 0.01s WALL ( 980 calls) + + General routines + calbec : 0.03s CPU 0.05s WALL ( 1125 calls) + fft : 0.01s CPU 0.05s WALL ( 50 calls) + fftw : 0.57s CPU 0.64s WALL ( 8656 calls) + davcio : 0.00s CPU 0.06s WALL ( 29 calls) + + Parallel routines + fft_scatter : 0.29s CPU 0.31s WALL ( 8706 calls) + + PWSCF : 1.07s CPU 2.22s WALL + + + This run was terminated on: 19:30: 3 27Sep2017 + +=------------------------------------------------------------------------------= + JOB DONE. +=------------------------------------------------------------------------------= diff --git a/capolanco/__pycache__/ioqeclass.cpython-39.pyc b/capolanco/__pycache__/ioqeclass.cpython-39.pyc new file mode 100644 index 0000000000000000000000000000000000000000..6c31709eab9824c949939c8e250b7c00b26c1d2e GIT binary patch literal 1529 zcmZ{kPjB2r6u@W3p0%@00#xNs5TFscU=*^IfQUnciYOrdXbVcYtb{DbGfCZgZSNaz zw^=!-^osZZRi%Uj5}$|LTsh?{*1VZ{Z{E|J`Mq(nvC(JPKK<*r^rJP# z{-(uh^KfwoyL}slW}4@0#J^!$XzwZ0-kBH)%@0`QU!t82QW%`4l&xATbr0_mKD{so_~G+L1tB&C)O%$Yzo<-v8sMx)KAl- zsHbD~m94;7TdLMU9hIOGRn2yvs5HsbX`a+sS)?2@xNbD}v44r(zJ;P@5BV`3?{`j# z{VEz33(e?Y!^pd&?Lb%23MaFo-uootn00+pnaFdZs75jYNKTx5bPSn}xbv;akN#v3 zqTkiM!Ozx!9i&NB=1Gy3gS%xq9h;)IgYU}2FRCif(l*b*IH^B|WB_JX)@IcsD<`JC zhTZDKg>jq}Sslmg7~aw~GjD!#d274Z=Cn1D8JonuJoX>BsPV{WoYN>4qu20f?0L81 z4cGpeI2Db!%YIR(UgMpM3wG)^KI}9|Zj0&OBLO>{O@@=5Mx1+SUGA#=bJ^{>;0=4& z({i6Jbio!|=z^s#TGP^|9J1);r)Y_uRWNaKiaz5>M{7K8a6ZohY>M^-DaAw~_!TgYieADaGD15%odxA8#=o9nJ ze<6}vN_BVLC;^Jt*6m9HiWdO#nm0mAM2UD2<%ft6Q8xYs!f*T*n`|WPHTVz_YJgDp z5bEJ%kM`*h@%dzV#`Ib{@2|{nwDa}nK^x6Gmjtfi-Pi)$7{U!q8>m?4?;@>(UEVz-gmDl2jtMgcucDu+0B{Wu<% zdYaRGJ&q^SBwtv9IM!tv$3Q<{*djrNv62Y=G=NA0l_;IZk}BlB4Ey2xtv2#TvY3vm YldeK( 1.29MB + + Estimated total allocated dynamical RAM > 31.06MB + + Initial potential from superposition of free atoms + + starting charge 7.99901, renormalised to 8.00000 + Starting wfc are 8 randomized atomic wfcs + + total cpu time spent up to now is 0.4 secs + + per-process dynamical memory: 2.9 Mb + + Self-consistent Calculation + + iteration # 1 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.00E-02, avg # of iterations = 2.0 + + Threshold (ethr) on eigenvalues was too large: + Diagonalizing with lowered threshold + + Davidson diagonalization with overlap + ethr = 7.97E-04, avg # of iterations = 1.0 + + total cpu time spent up to now is 0.6 secs + + total energy = -15.84982619 Ry + Harris-Foulkes estimate = -15.87079416 Ry + estimated scf accuracy < 0.06161703 Ry + + iteration # 2 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 7.70E-04, avg # of iterations = 1.0 + + total cpu time spent up to now is 0.7 secs + + total energy = -15.85288351 Ry + Harris-Foulkes estimate = -15.85318795 Ry + estimated scf accuracy < 0.00216687 Ry + + iteration # 3 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 2.71E-05, avg # of iterations = 2.4 + + total cpu time spent up to now is 0.8 secs + + total energy = -15.85332918 Ry + Harris-Foulkes estimate = -15.85336185 Ry + estimated scf accuracy < 0.00007437 Ry + + iteration # 4 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 9.30E-07, avg # of iterations = 2.1 + + total cpu time spent up to now is 0.8 secs + + total energy = -15.85334986 Ry + Harris-Foulkes estimate = -15.85335396 Ry + estimated scf accuracy < 0.00000888 Ry + + iteration # 5 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.11E-07, avg # of iterations = 2.1 + + total cpu time spent up to now is 0.9 secs + + total energy = -15.85335134 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 0.00000011 Ry + + iteration # 6 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.35E-09, avg # of iterations = 2.6 + + total cpu time spent up to now is 1.0 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 2.9E-09 Ry + + iteration # 7 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 3.68E-11, avg # of iterations = 2.6 + + total cpu time spent up to now is 1.1 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 2.9E-11 Ry + + iteration # 8 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 3.65E-13, avg # of iterations = 3.3 + + total cpu time spent up to now is 1.2 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 5.4E-12 Ry + + iteration # 9 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.00E-13, avg # of iterations = 1.7 + + total cpu time spent up to now is 1.3 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 1.2E-13 Ry + + iteration # 10 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.00E-13, avg # of iterations = 1.0 + + total cpu time spent up to now is 1.4 secs + + End of self-consistent calculation + + k = 0.0000 0.0000 0.0000 ( 4477 PWs) bands (ev): + + -5.8300 6.2061 6.2061 6.2061 + + k =-0.1250 0.1250-0.1250 ( 4507 PWs) bands (ev): + + -5.6230 4.6051 5.9132 5.9132 + + k =-0.2500 0.2500-0.2500 ( 4510 PWs) bands (ev): + + -5.0182 2.2559 5.4373 5.4373 + + k =-0.3750 0.3750-0.3750 ( 4501 PWs) bands (ev): + + -4.1058 0.2065 5.1074 5.1074 + + k = 0.5000-0.5000 0.5000 ( 4476 PWs) bands (ev): + + -3.4453 -0.8427 4.9947 4.9947 + + k = 0.0000 0.2500 0.0000 ( 4504 PWs) bands (ev): + + -5.5533 4.8935 5.3857 5.3857 + + k =-0.1250 0.3750-0.1250 ( 4517 PWs) bands (ev): + + -5.0777 2.9801 4.8669 4.9518 + + k =-0.2500 0.5000-0.2500 ( 4508 PWs) bands (ev): + + -4.2481 0.8896 4.3532 4.5964 + + k = 0.6250-0.3750 0.6250 ( 4486 PWs) bands (ev): + + -3.3613 -0.6068 3.9003 4.6231 + + k = 0.5000-0.2500 0.5000 ( 4491 PWs) bands (ev): + + -3.6148 -0.2257 3.7125 4.9256 + + k = 0.3750-0.1250 0.3750 ( 4497 PWs) bands (ev): + + -4.5602 1.5598 3.8591 5.4251 + + k = 0.2500 0.0000 0.2500 ( 4477 PWs) bands (ev): + + -5.2819 3.5267 4.5444 5.9125 + + k = 0.0000 0.5000 0.0000 ( 4520 PWs) bands (ev): + + -4.7329 2.7148 4.2862 4.2862 + + k =-0.1250 0.6250-0.1250 ( 4509 PWs) bands (ev): + + -4.0117 1.2745 3.4881 3.9636 + + k = 0.7500-0.2500 0.7500 ( 4482 PWs) bands (ev): + + -3.0647 -0.1975 2.6082 3.9678 + + k = 0.6250-0.1250 0.6250 ( 4477 PWs) bands (ev): + + -2.8512 -0.4657 2.1376 4.2926 + + k = 0.5000 0.0000 0.5000 ( 4489 PWs) bands (ev): + + -3.7521 0.7207 2.3750 4.8614 + + k = 0.0000 0.7500 0.0000 ( 4484 PWs) bands (ev): + + -3.4015 0.4708 3.5586 3.5586 + + k = 0.8750-0.1250 0.8750 ( 4479 PWs) bands (ev): + + -2.4888 -0.6253 2.7002 3.4815 + + k = 0.7500 0.0000 0.7500 ( 4454 PWs) bands (ev): + + -2.0305 -1.0339 1.8049 3.7440 + + k = 0.0000-1.0000 0.0000 ( 4456 PWs) bands (ev): + + -1.6267 -1.6267 3.3090 3.3090 + + k =-0.2500 0.5000 0.0000 ( 4503 PWs) bands (ev): + + -4.4807 1.9234 3.4393 4.7592 + + k = 0.6250-0.3750 0.8750 ( 4489 PWs) bands (ev): + + -3.5748 0.3447 2.8290 4.2439 + + k = 0.5000-0.2500 0.7500 ( 4486 PWs) bands (ev): + + -2.9014 -0.6278 2.7039 4.0076 + + k = 0.7500-0.2500 1.0000 ( 4484 PWs) bands (ev): + + -3.1970 0.2501 2.7770 3.3923 + + k = 0.6250-0.1250 0.8750 ( 4486 PWs) bands (ev): + + -2.3006 -0.7332 2.0576 3.1860 + + k = 0.5000 0.0000 0.7500 ( 4490 PWs) bands (ev): + + -2.6570 -0.3670 1.8851 3.5717 + + k =-0.2500-1.0000 0.0000 ( 4472 PWs) bands (ev): + + -1.5427 -1.5427 2.7194 2.7194 + + k =-0.5000-1.0000 0.0000 ( 4488 PWs) bands (ev): + + -1.4495 -1.4495 2.2655 2.2655 + + highest occupied level (ev): 6.2061 + +! total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 4.0E-15 Ry + + The total energy is the sum of the following terms: + + one-electron contribution = 4.76680131 Ry + hartree contribution = 1.08149972 Ry + xc contribution = -4.81476914 Ry + ewald contribution = -16.88688327 Ry + + convergence has been achieved in 10 iterations + + Forces acting on atoms (cartesian axes, Ry/au): + + atom 1 type 1 force = 0.00000000 0.00000000 0.00000000 + atom 2 type 1 force = 0.00000000 0.00000000 -0.00000000 + + Total force = 0.000000 Total SCF correction = 0.000000 + + + Computing stress (Cartesian axis) and pressure + + total stress (Ry/bohr**3) (kbar) P= 0.05 + 0.00000032 -0.00000000 -0.00000000 0.05 -0.00 -0.00 + -0.00000000 0.00000032 0.00000000 -0.00 0.05 0.00 + -0.00000000 0.00000000 0.00000032 -0.00 0.00 0.05 + + + Writing output data file Si.save + + init_run : 0.06s CPU 0.23s WALL ( 1 calls) + electrons : 0.85s CPU 1.01s WALL ( 1 calls) + forces : 0.00s CPU 0.01s WALL ( 1 calls) + stress : 0.02s CPU 0.03s WALL ( 1 calls) + + Called by init_run: + wfcinit : 0.04s CPU 0.11s WALL ( 1 calls) + potinit : 0.00s CPU 0.01s WALL ( 1 calls) + + Called by electrons: + c_bands : 0.73s CPU 0.80s WALL ( 11 calls) + sum_band : 0.11s CPU 0.13s WALL ( 11 calls) + v_of_rho : 0.00s CPU 0.01s WALL ( 11 calls) + mix_rho : 0.00s CPU 0.01s WALL ( 11 calls) + + Called by c_bands: + init_us_2 : 0.01s CPU 0.03s WALL ( 725 calls) + cegterg : 0.69s CPU 0.74s WALL ( 319 calls) + + Called by sum_band: + + Called by *egterg: + h_psi : 0.62s CPU 0.65s WALL ( 980 calls) + g_psi : 0.00s CPU 0.00s WALL ( 632 calls) + cdiaghg : 0.05s CPU 0.10s WALL ( 922 calls) + + Called by h_psi: + h_psi:pot : 0.61s CPU 0.65s WALL ( 980 calls) + h_psi:calbec : 0.03s CPU 0.04s WALL ( 980 calls) + vloc_psi : 0.57s CPU 0.59s WALL ( 980 calls) + add_vuspsi : 0.01s CPU 0.01s WALL ( 980 calls) + + General routines + calbec : 0.03s CPU 0.05s WALL ( 1125 calls) + fft : 0.01s CPU 0.05s WALL ( 50 calls) + fftw : 0.57s CPU 0.64s WALL ( 8656 calls) + davcio : 0.00s CPU 0.06s WALL ( 29 calls) + + Parallel routines + fft_scatter : 0.29s CPU 0.31s WALL ( 8706 calls) + + PWSCF : 1.07s CPU 2.22s WALL + + + This run was terminated on: 19:30: 3 27Sep2017 + +=------------------------------------------------------------------------------= + JOB DONE. +=------------------------------------------------------------------------------= From 4932df23a15f043acec160e9f6eb34d4ae25f8a7 Mon Sep 17 00:00:00 2001 From: cpolanco Date: Wed, 7 Dec 2022 23:47:09 +0100 Subject: [PATCH 2/3] The core convergence program is working. The code iterates on fictituos files until achieving convergence. This program should work in principle for any valid input given in QE --- capolanco/RunConvergence.py | 59 ++- .../__pycache__/ioqeclass.cpython-39.pyc | Bin 1529 -> 2292 bytes capolanco/ioqeclass.py | 42 ++ capolanco/test.scf1.in | 30 ++ capolanco/test.scf1.out | 437 ++++++++++++++++++ capolanco/test.scf2.in | 30 ++ capolanco/test.scf2.out | 437 ++++++++++++++++++ capolanco/test.scf3.in | 30 ++ capolanco/test.scf3.out | 437 ++++++++++++++++++ capolanco/test.scf4.in | 30 ++ capolanco/test.scf4.out | 437 ++++++++++++++++++ 11 files changed, 1957 insertions(+), 12 deletions(-) create mode 100644 capolanco/test.scf1.in create mode 100644 capolanco/test.scf1.out create mode 100644 capolanco/test.scf2.in create mode 100644 capolanco/test.scf2.out create mode 100644 capolanco/test.scf3.in create mode 100644 capolanco/test.scf3.out create mode 100644 capolanco/test.scf4.in create mode 100644 capolanco/test.scf4.out diff --git a/capolanco/RunConvergence.py b/capolanco/RunConvergence.py index f9256a09..b78b0abd 100644 --- a/capolanco/RunConvergence.py +++ b/capolanco/RunConvergence.py @@ -14,9 +14,17 @@ # Define delta energy threshold for # convergence (eV) -dE=1 # (eV) +dEthreshold=1.0 # (eV) +########################### +##### DEVELOPERS INPUTS +########################### + +# maximum of iterations +Nitermax=20 +# increasing step of kgrid +kstep=2 ########################### ##### PROGRAM @@ -34,20 +42,47 @@ qeinput.save(filein,testin) # Run initial test ##### pw.x test.scf.in test.scf.out +# Initialize pw.x output class +qeoutput=qe.qepwoutput() # Read the Total energy from the output +qeoutput.getenergy(testout) # Loop testing for dE - -## set up calculation -#fileout='test.scf.in' -#qeinput.save(filein,fileout) - -## run pw.x - -## extract the total energy - -## compare with the threshold - +dE=2.0*dEthreshold +EnergyOld=qeoutput.energy +counter=0 +while ((dE>dEthreshold) and (counterG(#D!j9#ujQT*4odz-^|X;&dmPK{hG@=Gc#EN<4-ZF z74lJjk*-9mrQ$;(48h(L!QN>*x}eX9ZAOoN+7r6NMA-MGt;br+kC~&C(~sG{s~TcL zV?u4k^k)&T}$pp*FK(GK}R`c3{oG_IgZ|UV+4h0EJAJue=nt3G7jXOqVG>iJQ zrzlc$00WKlW6G6|#Car4zJZ@@sseIFfSC1EBa~_$33RD00)PhIF}6b4^gRdUB@~qr zE+H%;oQj5!ae+0j%pkplaP_Q08uR!gyBs|(Qy%RvZ$g4HakeA*`mlJKXtRa#fDHMmu&@Tbxdjh4&9cIbFKjhpYPc9Z+P^|zQ1$X`nAHXv;Zdm(9r zW4ipq7{Si{{`FIR>CWn1J9AR}wCYJpR`7(4fb~}k2xsa`;we{#sqcM|2B<UMO p$|js`?66k1>G#v3Vl@)}KO@+-v9;N3i>@cP@O=dM!Yr15@fQd7%H99~ delta 371 zcmZvYKTg9i6o=zDFLenC6!9+=DnU#ZLSkX7H~||A$`&;SRU~bANmZpwkAR|_f`O?Q z;0|m)24aB;zp{XYEq%lH`^kRxNAJ@M65rpj%({Gg8l88W;E45`v(Qc1jU}Dt_FYOA zLt52^l3d%9B8CJpsWm*@<2aQ}JEh9*o-GuslD)DJ%vtCVTmucGY+5P_*lDkM-xCz9 z(Oo@q!Ca5TX1jDwmp=8`92u#=U|~nm7mJXS*dpOZ7qq2|+vIu%8s<2z6z-6qD{ 1.29MB + + Estimated total allocated dynamical RAM > 31.06MB + + Initial potential from superposition of free atoms + + starting charge 7.99901, renormalised to 8.00000 + Starting wfc are 8 randomized atomic wfcs + + total cpu time spent up to now is 0.4 secs + + per-process dynamical memory: 2.9 Mb + + Self-consistent Calculation + + iteration # 1 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.00E-02, avg # of iterations = 2.0 + + Threshold (ethr) on eigenvalues was too large: + Diagonalizing with lowered threshold + + Davidson diagonalization with overlap + ethr = 7.97E-04, avg # of iterations = 1.0 + + total cpu time spent up to now is 0.6 secs + + total energy = -15.84982619 Ry + Harris-Foulkes estimate = -15.87079416 Ry + estimated scf accuracy < 0.06161703 Ry + + iteration # 2 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 7.70E-04, avg # of iterations = 1.0 + + total cpu time spent up to now is 0.7 secs + + total energy = -15.85288351 Ry + Harris-Foulkes estimate = -15.85318795 Ry + estimated scf accuracy < 0.00216687 Ry + + iteration # 3 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 2.71E-05, avg # of iterations = 2.4 + + total cpu time spent up to now is 0.8 secs + + total energy = -15.85332918 Ry + Harris-Foulkes estimate = -15.85336185 Ry + estimated scf accuracy < 0.00007437 Ry + + iteration # 4 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 9.30E-07, avg # of iterations = 2.1 + + total cpu time spent up to now is 0.8 secs + + total energy = -15.85334986 Ry + Harris-Foulkes estimate = -15.85335396 Ry + estimated scf accuracy < 0.00000888 Ry + + iteration # 5 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.11E-07, avg # of iterations = 2.1 + + total cpu time spent up to now is 0.9 secs + + total energy = -15.85335134 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 0.00000011 Ry + + iteration # 6 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.35E-09, avg # of iterations = 2.6 + + total cpu time spent up to now is 1.0 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 2.9E-09 Ry + + iteration # 7 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 3.68E-11, avg # of iterations = 2.6 + + total cpu time spent up to now is 1.1 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 2.9E-11 Ry + + iteration # 8 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 3.65E-13, avg # of iterations = 3.3 + + total cpu time spent up to now is 1.2 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 5.4E-12 Ry + + iteration # 9 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.00E-13, avg # of iterations = 1.7 + + total cpu time spent up to now is 1.3 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 1.2E-13 Ry + + iteration # 10 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.00E-13, avg # of iterations = 1.0 + + total cpu time spent up to now is 1.4 secs + + End of self-consistent calculation + + k = 0.0000 0.0000 0.0000 ( 4477 PWs) bands (ev): + + -5.8300 6.2061 6.2061 6.2061 + + k =-0.1250 0.1250-0.1250 ( 4507 PWs) bands (ev): + + -5.6230 4.6051 5.9132 5.9132 + + k =-0.2500 0.2500-0.2500 ( 4510 PWs) bands (ev): + + -5.0182 2.2559 5.4373 5.4373 + + k =-0.3750 0.3750-0.3750 ( 4501 PWs) bands (ev): + + -4.1058 0.2065 5.1074 5.1074 + + k = 0.5000-0.5000 0.5000 ( 4476 PWs) bands (ev): + + -3.4453 -0.8427 4.9947 4.9947 + + k = 0.0000 0.2500 0.0000 ( 4504 PWs) bands (ev): + + -5.5533 4.8935 5.3857 5.3857 + + k =-0.1250 0.3750-0.1250 ( 4517 PWs) bands (ev): + + -5.0777 2.9801 4.8669 4.9518 + + k =-0.2500 0.5000-0.2500 ( 4508 PWs) bands (ev): + + -4.2481 0.8896 4.3532 4.5964 + + k = 0.6250-0.3750 0.6250 ( 4486 PWs) bands (ev): + + -3.3613 -0.6068 3.9003 4.6231 + + k = 0.5000-0.2500 0.5000 ( 4491 PWs) bands (ev): + + -3.6148 -0.2257 3.7125 4.9256 + + k = 0.3750-0.1250 0.3750 ( 4497 PWs) bands (ev): + + -4.5602 1.5598 3.8591 5.4251 + + k = 0.2500 0.0000 0.2500 ( 4477 PWs) bands (ev): + + -5.2819 3.5267 4.5444 5.9125 + + k = 0.0000 0.5000 0.0000 ( 4520 PWs) bands (ev): + + -4.7329 2.7148 4.2862 4.2862 + + k =-0.1250 0.6250-0.1250 ( 4509 PWs) bands (ev): + + -4.0117 1.2745 3.4881 3.9636 + + k = 0.7500-0.2500 0.7500 ( 4482 PWs) bands (ev): + + -3.0647 -0.1975 2.6082 3.9678 + + k = 0.6250-0.1250 0.6250 ( 4477 PWs) bands (ev): + + -2.8512 -0.4657 2.1376 4.2926 + + k = 0.5000 0.0000 0.5000 ( 4489 PWs) bands (ev): + + -3.7521 0.7207 2.3750 4.8614 + + k = 0.0000 0.7500 0.0000 ( 4484 PWs) bands (ev): + + -3.4015 0.4708 3.5586 3.5586 + + k = 0.8750-0.1250 0.8750 ( 4479 PWs) bands (ev): + + -2.4888 -0.6253 2.7002 3.4815 + + k = 0.7500 0.0000 0.7500 ( 4454 PWs) bands (ev): + + -2.0305 -1.0339 1.8049 3.7440 + + k = 0.0000-1.0000 0.0000 ( 4456 PWs) bands (ev): + + -1.6267 -1.6267 3.3090 3.3090 + + k =-0.2500 0.5000 0.0000 ( 4503 PWs) bands (ev): + + -4.4807 1.9234 3.4393 4.7592 + + k = 0.6250-0.3750 0.8750 ( 4489 PWs) bands (ev): + + -3.5748 0.3447 2.8290 4.2439 + + k = 0.5000-0.2500 0.7500 ( 4486 PWs) bands (ev): + + -2.9014 -0.6278 2.7039 4.0076 + + k = 0.7500-0.2500 1.0000 ( 4484 PWs) bands (ev): + + -3.1970 0.2501 2.7770 3.3923 + + k = 0.6250-0.1250 0.8750 ( 4486 PWs) bands (ev): + + -2.3006 -0.7332 2.0576 3.1860 + + k = 0.5000 0.0000 0.7500 ( 4490 PWs) bands (ev): + + -2.6570 -0.3670 1.8851 3.5717 + + k =-0.2500-1.0000 0.0000 ( 4472 PWs) bands (ev): + + -1.5427 -1.5427 2.7194 2.7194 + + k =-0.5000-1.0000 0.0000 ( 4488 PWs) bands (ev): + + -1.4495 -1.4495 2.2655 2.2655 + + highest occupied level (ev): 6.2061 + +! total energy = -16.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 4.0E-15 Ry + + The total energy is the sum of the following terms: + + one-electron contribution = 4.76680131 Ry + hartree contribution = 1.08149972 Ry + xc contribution = -4.81476914 Ry + ewald contribution = -16.88688327 Ry + + convergence has been achieved in 10 iterations + + Forces acting on atoms (cartesian axes, Ry/au): + + atom 1 type 1 force = 0.00000000 0.00000000 0.00000000 + atom 2 type 1 force = 0.00000000 0.00000000 -0.00000000 + + Total force = 0.000000 Total SCF correction = 0.000000 + + + Computing stress (Cartesian axis) and pressure + + total stress (Ry/bohr**3) (kbar) P= 0.05 + 0.00000032 -0.00000000 -0.00000000 0.05 -0.00 -0.00 + -0.00000000 0.00000032 0.00000000 -0.00 0.05 0.00 + -0.00000000 0.00000000 0.00000032 -0.00 0.00 0.05 + + + Writing output data file Si.save + + init_run : 0.06s CPU 0.23s WALL ( 1 calls) + electrons : 0.85s CPU 1.01s WALL ( 1 calls) + forces : 0.00s CPU 0.01s WALL ( 1 calls) + stress : 0.02s CPU 0.03s WALL ( 1 calls) + + Called by init_run: + wfcinit : 0.04s CPU 0.11s WALL ( 1 calls) + potinit : 0.00s CPU 0.01s WALL ( 1 calls) + + Called by electrons: + c_bands : 0.73s CPU 0.80s WALL ( 11 calls) + sum_band : 0.11s CPU 0.13s WALL ( 11 calls) + v_of_rho : 0.00s CPU 0.01s WALL ( 11 calls) + mix_rho : 0.00s CPU 0.01s WALL ( 11 calls) + + Called by c_bands: + init_us_2 : 0.01s CPU 0.03s WALL ( 725 calls) + cegterg : 0.69s CPU 0.74s WALL ( 319 calls) + + Called by sum_band: + + Called by *egterg: + h_psi : 0.62s CPU 0.65s WALL ( 980 calls) + g_psi : 0.00s CPU 0.00s WALL ( 632 calls) + cdiaghg : 0.05s CPU 0.10s WALL ( 922 calls) + + Called by h_psi: + h_psi:pot : 0.61s CPU 0.65s WALL ( 980 calls) + h_psi:calbec : 0.03s CPU 0.04s WALL ( 980 calls) + vloc_psi : 0.57s CPU 0.59s WALL ( 980 calls) + add_vuspsi : 0.01s CPU 0.01s WALL ( 980 calls) + + General routines + calbec : 0.03s CPU 0.05s WALL ( 1125 calls) + fft : 0.01s CPU 0.05s WALL ( 50 calls) + fftw : 0.57s CPU 0.64s WALL ( 8656 calls) + davcio : 0.00s CPU 0.06s WALL ( 29 calls) + + Parallel routines + fft_scatter : 0.29s CPU 0.31s WALL ( 8706 calls) + + PWSCF : 1.07s CPU 2.22s WALL + + + This run was terminated on: 19:30: 3 27Sep2017 + +=------------------------------------------------------------------------------= + JOB DONE. +=------------------------------------------------------------------------------= diff --git a/capolanco/test.scf2.in b/capolanco/test.scf2.in new file mode 100644 index 00000000..529f9f22 --- /dev/null +++ b/capolanco/test.scf2.in @@ -0,0 +1,30 @@ + &control + calculation='scf', + outdir = '/global/cscratch1/sd/cpolanco/Si/', + prefix='Si', + pseudo_dir = '/global/homes/c/cpolanco/Materials/pseudo/', + restart_mode='from_scratch', + tprnfor= .true., + tstress= .true., + / + &system + ibrav= 2, + celldm(1)= 10.20777693, + nat= 2, + ntyp= 1, + ecutwfc= 100.0 + / + &electrons + mixing_beta= 0.7 + conv_thr= 1.0d-14 + / + +ATOMIC_SPECIES + Si 28.086 Si.pz-vbc.UPF + +ATOMIC_POSITIONS (alat) + Si 0.00 0.00 0.00 + Si 0.25 0.25 0.25 + +K_POINTS (automatic) + 12 12 12 0 0 0 \ No newline at end of file diff --git a/capolanco/test.scf2.out b/capolanco/test.scf2.out new file mode 100644 index 00000000..ce5f954a --- /dev/null +++ b/capolanco/test.scf2.out @@ -0,0 +1,437 @@ + + Program PWSCF v.6.1 starts on 27Sep2017 at 19:30: 1 + + 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); + 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 & OpenMP), running on 24 processor cores + Number of MPI processes: 24 + Threads/MPI process: 1 + R & G space division: proc/nbgrp/npool/nimage = 24 + Waiting for input... + Reading input from standard input + + 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 + + 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 59 59 17 1489 1489 232 + Max 60 60 18 1494 1494 235 + Sum 1417 1417 421 35749 35749 5601 + + + + bravais-lattice index = 2 + lattice parameter (alat) = 10.2078 a.u. + unit-cell volume = 265.9093 (a.u.)^3 + number of atoms/cell = 2 + number of atomic types = 1 + number of electrons = 8.00 + number of Kohn-Sham states= 4 + kinetic-energy cutoff = 100.0000 Ry + charge density cutoff = 400.0000 Ry + convergence threshold = 1.0E-14 + mixing beta = 0.7000 + number of iterations used = 8 plain mixing + Exchange-correlation = SLA PZ NOGX NOGC ( 1 1 0 0 0 0) + + celldm(1)= 10.207777 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) = ( -0.500000 0.000000 0.500000 ) + a(2) = ( 0.000000 0.500000 0.500000 ) + a(3) = ( -0.500000 0.500000 0.000000 ) + + reciprocal axes: (cart. coord. in units 2 pi/alat) + b(1) = ( -1.000000 -1.000000 1.000000 ) + b(2) = ( 1.000000 1.000000 1.000000 ) + b(3) = ( -1.000000 1.000000 -1.000000 ) + + + PseudoPot. # 1 for Si read from file: + /global/homes/c/cpolanco/Materials/pseudo/Si.pz-vbc.UPF + MD5 check sum: 6dfa03ddd5817404712e03e4d12deb78 + Pseudo is Norm-conserving, Zval = 4.0 + Generated by new atomic code, or converted to UPF format + Using radial grid of 431 points, 2 beta functions with: + l(1) = 0 + l(2) = 1 + + atomic species valence mass pseudopotential + Si 4.00 28.08600 Si( 1.00) + + 24 Sym. Ops. (no inversion) found + (note: 24 additional sym.ops. were found but ignored + their fractional translations are incommensurate with FFT grid) + + + Cartesian axes + + site n. atom positions (alat units) + 1 Si tau( 1) = ( 0.0000000 0.0000000 0.0000000 ) + 2 Si tau( 2) = ( 0.2500000 0.2500000 0.2500000 ) + + number of k points= 29 + cart. coord. in units 2pi/alat + k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 0.0039062 + k( 2) = ( -0.1250000 0.1250000 -0.1250000), wk = 0.0312500 + k( 3) = ( -0.2500000 0.2500000 -0.2500000), wk = 0.0312500 + k( 4) = ( -0.3750000 0.3750000 -0.3750000), wk = 0.0312500 + k( 5) = ( 0.5000000 -0.5000000 0.5000000), wk = 0.0156250 + k( 6) = ( 0.0000000 0.2500000 0.0000000), wk = 0.0234375 + k( 7) = ( -0.1250000 0.3750000 -0.1250000), wk = 0.0937500 + k( 8) = ( -0.2500000 0.5000000 -0.2500000), wk = 0.0937500 + k( 9) = ( 0.6250000 -0.3750000 0.6250000), wk = 0.0937500 + k( 10) = ( 0.5000000 -0.2500000 0.5000000), wk = 0.0937500 + k( 11) = ( 0.3750000 -0.1250000 0.3750000), wk = 0.0937500 + k( 12) = ( 0.2500000 0.0000000 0.2500000), wk = 0.0468750 + k( 13) = ( 0.0000000 0.5000000 0.0000000), wk = 0.0234375 + k( 14) = ( -0.1250000 0.6250000 -0.1250000), wk = 0.0937500 + k( 15) = ( 0.7500000 -0.2500000 0.7500000), wk = 0.0937500 + k( 16) = ( 0.6250000 -0.1250000 0.6250000), wk = 0.0937500 + k( 17) = ( 0.5000000 0.0000000 0.5000000), wk = 0.0468750 + k( 18) = ( 0.0000000 0.7500000 0.0000000), wk = 0.0234375 + k( 19) = ( 0.8750000 -0.1250000 0.8750000), wk = 0.0937500 + k( 20) = ( 0.7500000 0.0000000 0.7500000), wk = 0.0468750 + k( 21) = ( 0.0000000 -1.0000000 0.0000000), wk = 0.0117188 + k( 22) = ( -0.2500000 0.5000000 0.0000000), wk = 0.0937500 + k( 23) = ( 0.6250000 -0.3750000 0.8750000), wk = 0.1875000 + k( 24) = ( 0.5000000 -0.2500000 0.7500000), wk = 0.0937500 + k( 25) = ( 0.7500000 -0.2500000 1.0000000), wk = 0.0937500 + k( 26) = ( 0.6250000 -0.1250000 0.8750000), wk = 0.1875000 + k( 27) = ( 0.5000000 0.0000000 0.7500000), wk = 0.0937500 + k( 28) = ( -0.2500000 -1.0000000 0.0000000), wk = 0.0468750 + k( 29) = ( -0.5000000 -1.0000000 0.0000000), wk = 0.0234375 + + Dense grid: 35749 G-vectors FFT dimensions: ( 45, 45, 45) + + Estimated max dynamical RAM per process > 1.29MB + + Estimated total allocated dynamical RAM > 31.06MB + + Initial potential from superposition of free atoms + + starting charge 7.99901, renormalised to 8.00000 + Starting wfc are 8 randomized atomic wfcs + + total cpu time spent up to now is 0.4 secs + + per-process dynamical memory: 2.9 Mb + + Self-consistent Calculation + + iteration # 1 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.00E-02, avg # of iterations = 2.0 + + Threshold (ethr) on eigenvalues was too large: + Diagonalizing with lowered threshold + + Davidson diagonalization with overlap + ethr = 7.97E-04, avg # of iterations = 1.0 + + total cpu time spent up to now is 0.6 secs + + total energy = -15.84982619 Ry + Harris-Foulkes estimate = -15.87079416 Ry + estimated scf accuracy < 0.06161703 Ry + + iteration # 2 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 7.70E-04, avg # of iterations = 1.0 + + total cpu time spent up to now is 0.7 secs + + total energy = -15.85288351 Ry + Harris-Foulkes estimate = -15.85318795 Ry + estimated scf accuracy < 0.00216687 Ry + + iteration # 3 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 2.71E-05, avg # of iterations = 2.4 + + total cpu time spent up to now is 0.8 secs + + total energy = -15.85332918 Ry + Harris-Foulkes estimate = -15.85336185 Ry + estimated scf accuracy < 0.00007437 Ry + + iteration # 4 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 9.30E-07, avg # of iterations = 2.1 + + total cpu time spent up to now is 0.8 secs + + total energy = -15.85334986 Ry + Harris-Foulkes estimate = -15.85335396 Ry + estimated scf accuracy < 0.00000888 Ry + + iteration # 5 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.11E-07, avg # of iterations = 2.1 + + total cpu time spent up to now is 0.9 secs + + total energy = -15.85335134 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 0.00000011 Ry + + iteration # 6 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.35E-09, avg # of iterations = 2.6 + + total cpu time spent up to now is 1.0 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 2.9E-09 Ry + + iteration # 7 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 3.68E-11, avg # of iterations = 2.6 + + total cpu time spent up to now is 1.1 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 2.9E-11 Ry + + iteration # 8 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 3.65E-13, avg # of iterations = 3.3 + + total cpu time spent up to now is 1.2 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 5.4E-12 Ry + + iteration # 9 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.00E-13, avg # of iterations = 1.7 + + total cpu time spent up to now is 1.3 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 1.2E-13 Ry + + iteration # 10 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.00E-13, avg # of iterations = 1.0 + + total cpu time spent up to now is 1.4 secs + + End of self-consistent calculation + + k = 0.0000 0.0000 0.0000 ( 4477 PWs) bands (ev): + + -5.8300 6.2061 6.2061 6.2061 + + k =-0.1250 0.1250-0.1250 ( 4507 PWs) bands (ev): + + -5.6230 4.6051 5.9132 5.9132 + + k =-0.2500 0.2500-0.2500 ( 4510 PWs) bands (ev): + + -5.0182 2.2559 5.4373 5.4373 + + k =-0.3750 0.3750-0.3750 ( 4501 PWs) bands (ev): + + -4.1058 0.2065 5.1074 5.1074 + + k = 0.5000-0.5000 0.5000 ( 4476 PWs) bands (ev): + + -3.4453 -0.8427 4.9947 4.9947 + + k = 0.0000 0.2500 0.0000 ( 4504 PWs) bands (ev): + + -5.5533 4.8935 5.3857 5.3857 + + k =-0.1250 0.3750-0.1250 ( 4517 PWs) bands (ev): + + -5.0777 2.9801 4.8669 4.9518 + + k =-0.2500 0.5000-0.2500 ( 4508 PWs) bands (ev): + + -4.2481 0.8896 4.3532 4.5964 + + k = 0.6250-0.3750 0.6250 ( 4486 PWs) bands (ev): + + -3.3613 -0.6068 3.9003 4.6231 + + k = 0.5000-0.2500 0.5000 ( 4491 PWs) bands (ev): + + -3.6148 -0.2257 3.7125 4.9256 + + k = 0.3750-0.1250 0.3750 ( 4497 PWs) bands (ev): + + -4.5602 1.5598 3.8591 5.4251 + + k = 0.2500 0.0000 0.2500 ( 4477 PWs) bands (ev): + + -5.2819 3.5267 4.5444 5.9125 + + k = 0.0000 0.5000 0.0000 ( 4520 PWs) bands (ev): + + -4.7329 2.7148 4.2862 4.2862 + + k =-0.1250 0.6250-0.1250 ( 4509 PWs) bands (ev): + + -4.0117 1.2745 3.4881 3.9636 + + k = 0.7500-0.2500 0.7500 ( 4482 PWs) bands (ev): + + -3.0647 -0.1975 2.6082 3.9678 + + k = 0.6250-0.1250 0.6250 ( 4477 PWs) bands (ev): + + -2.8512 -0.4657 2.1376 4.2926 + + k = 0.5000 0.0000 0.5000 ( 4489 PWs) bands (ev): + + -3.7521 0.7207 2.3750 4.8614 + + k = 0.0000 0.7500 0.0000 ( 4484 PWs) bands (ev): + + -3.4015 0.4708 3.5586 3.5586 + + k = 0.8750-0.1250 0.8750 ( 4479 PWs) bands (ev): + + -2.4888 -0.6253 2.7002 3.4815 + + k = 0.7500 0.0000 0.7500 ( 4454 PWs) bands (ev): + + -2.0305 -1.0339 1.8049 3.7440 + + k = 0.0000-1.0000 0.0000 ( 4456 PWs) bands (ev): + + -1.6267 -1.6267 3.3090 3.3090 + + k =-0.2500 0.5000 0.0000 ( 4503 PWs) bands (ev): + + -4.4807 1.9234 3.4393 4.7592 + + k = 0.6250-0.3750 0.8750 ( 4489 PWs) bands (ev): + + -3.5748 0.3447 2.8290 4.2439 + + k = 0.5000-0.2500 0.7500 ( 4486 PWs) bands (ev): + + -2.9014 -0.6278 2.7039 4.0076 + + k = 0.7500-0.2500 1.0000 ( 4484 PWs) bands (ev): + + -3.1970 0.2501 2.7770 3.3923 + + k = 0.6250-0.1250 0.8750 ( 4486 PWs) bands (ev): + + -2.3006 -0.7332 2.0576 3.1860 + + k = 0.5000 0.0000 0.7500 ( 4490 PWs) bands (ev): + + -2.6570 -0.3670 1.8851 3.5717 + + k =-0.2500-1.0000 0.0000 ( 4472 PWs) bands (ev): + + -1.5427 -1.5427 2.7194 2.7194 + + k =-0.5000-1.0000 0.0000 ( 4488 PWs) bands (ev): + + -1.4495 -1.4495 2.2655 2.2655 + + highest occupied level (ev): 6.2061 + +! total energy = -15.95335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 4.0E-15 Ry + + The total energy is the sum of the following terms: + + one-electron contribution = 4.76680131 Ry + hartree contribution = 1.08149972 Ry + xc contribution = -4.81476914 Ry + ewald contribution = -16.88688327 Ry + + convergence has been achieved in 10 iterations + + Forces acting on atoms (cartesian axes, Ry/au): + + atom 1 type 1 force = 0.00000000 0.00000000 0.00000000 + atom 2 type 1 force = 0.00000000 0.00000000 -0.00000000 + + Total force = 0.000000 Total SCF correction = 0.000000 + + + Computing stress (Cartesian axis) and pressure + + total stress (Ry/bohr**3) (kbar) P= 0.05 + 0.00000032 -0.00000000 -0.00000000 0.05 -0.00 -0.00 + -0.00000000 0.00000032 0.00000000 -0.00 0.05 0.00 + -0.00000000 0.00000000 0.00000032 -0.00 0.00 0.05 + + + Writing output data file Si.save + + init_run : 0.06s CPU 0.23s WALL ( 1 calls) + electrons : 0.85s CPU 1.01s WALL ( 1 calls) + forces : 0.00s CPU 0.01s WALL ( 1 calls) + stress : 0.02s CPU 0.03s WALL ( 1 calls) + + Called by init_run: + wfcinit : 0.04s CPU 0.11s WALL ( 1 calls) + potinit : 0.00s CPU 0.01s WALL ( 1 calls) + + Called by electrons: + c_bands : 0.73s CPU 0.80s WALL ( 11 calls) + sum_band : 0.11s CPU 0.13s WALL ( 11 calls) + v_of_rho : 0.00s CPU 0.01s WALL ( 11 calls) + mix_rho : 0.00s CPU 0.01s WALL ( 11 calls) + + Called by c_bands: + init_us_2 : 0.01s CPU 0.03s WALL ( 725 calls) + cegterg : 0.69s CPU 0.74s WALL ( 319 calls) + + Called by sum_band: + + Called by *egterg: + h_psi : 0.62s CPU 0.65s WALL ( 980 calls) + g_psi : 0.00s CPU 0.00s WALL ( 632 calls) + cdiaghg : 0.05s CPU 0.10s WALL ( 922 calls) + + Called by h_psi: + h_psi:pot : 0.61s CPU 0.65s WALL ( 980 calls) + h_psi:calbec : 0.03s CPU 0.04s WALL ( 980 calls) + vloc_psi : 0.57s CPU 0.59s WALL ( 980 calls) + add_vuspsi : 0.01s CPU 0.01s WALL ( 980 calls) + + General routines + calbec : 0.03s CPU 0.05s WALL ( 1125 calls) + fft : 0.01s CPU 0.05s WALL ( 50 calls) + fftw : 0.57s CPU 0.64s WALL ( 8656 calls) + davcio : 0.00s CPU 0.06s WALL ( 29 calls) + + Parallel routines + fft_scatter : 0.29s CPU 0.31s WALL ( 8706 calls) + + PWSCF : 1.07s CPU 2.22s WALL + + + This run was terminated on: 19:30: 3 27Sep2017 + +=------------------------------------------------------------------------------= + JOB DONE. +=------------------------------------------------------------------------------= diff --git a/capolanco/test.scf3.in b/capolanco/test.scf3.in new file mode 100644 index 00000000..ef5210f4 --- /dev/null +++ b/capolanco/test.scf3.in @@ -0,0 +1,30 @@ + &control + calculation='scf', + outdir = '/global/cscratch1/sd/cpolanco/Si/', + prefix='Si', + pseudo_dir = '/global/homes/c/cpolanco/Materials/pseudo/', + restart_mode='from_scratch', + tprnfor= .true., + tstress= .true., + / + &system + ibrav= 2, + celldm(1)= 10.20777693, + nat= 2, + ntyp= 1, + ecutwfc= 100.0 + / + &electrons + mixing_beta= 0.7 + conv_thr= 1.0d-14 + / + +ATOMIC_SPECIES + Si 28.086 Si.pz-vbc.UPF + +ATOMIC_POSITIONS (alat) + Si 0.00 0.00 0.00 + Si 0.25 0.25 0.25 + +K_POINTS (automatic) + 14 14 14 0 0 0 \ No newline at end of file diff --git a/capolanco/test.scf3.out b/capolanco/test.scf3.out new file mode 100644 index 00000000..24c158b7 --- /dev/null +++ b/capolanco/test.scf3.out @@ -0,0 +1,437 @@ + + Program PWSCF v.6.1 starts on 27Sep2017 at 19:30: 1 + + 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); + 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 & OpenMP), running on 24 processor cores + Number of MPI processes: 24 + Threads/MPI process: 1 + R & G space division: proc/nbgrp/npool/nimage = 24 + Waiting for input... + Reading input from standard input + + 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 + + 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 59 59 17 1489 1489 232 + Max 60 60 18 1494 1494 235 + Sum 1417 1417 421 35749 35749 5601 + + + + bravais-lattice index = 2 + lattice parameter (alat) = 10.2078 a.u. + unit-cell volume = 265.9093 (a.u.)^3 + number of atoms/cell = 2 + number of atomic types = 1 + number of electrons = 8.00 + number of Kohn-Sham states= 4 + kinetic-energy cutoff = 100.0000 Ry + charge density cutoff = 400.0000 Ry + convergence threshold = 1.0E-14 + mixing beta = 0.7000 + number of iterations used = 8 plain mixing + Exchange-correlation = SLA PZ NOGX NOGC ( 1 1 0 0 0 0) + + celldm(1)= 10.207777 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) = ( -0.500000 0.000000 0.500000 ) + a(2) = ( 0.000000 0.500000 0.500000 ) + a(3) = ( -0.500000 0.500000 0.000000 ) + + reciprocal axes: (cart. coord. in units 2 pi/alat) + b(1) = ( -1.000000 -1.000000 1.000000 ) + b(2) = ( 1.000000 1.000000 1.000000 ) + b(3) = ( -1.000000 1.000000 -1.000000 ) + + + PseudoPot. # 1 for Si read from file: + /global/homes/c/cpolanco/Materials/pseudo/Si.pz-vbc.UPF + MD5 check sum: 6dfa03ddd5817404712e03e4d12deb78 + Pseudo is Norm-conserving, Zval = 4.0 + Generated by new atomic code, or converted to UPF format + Using radial grid of 431 points, 2 beta functions with: + l(1) = 0 + l(2) = 1 + + atomic species valence mass pseudopotential + Si 4.00 28.08600 Si( 1.00) + + 24 Sym. Ops. (no inversion) found + (note: 24 additional sym.ops. were found but ignored + their fractional translations are incommensurate with FFT grid) + + + Cartesian axes + + site n. atom positions (alat units) + 1 Si tau( 1) = ( 0.0000000 0.0000000 0.0000000 ) + 2 Si tau( 2) = ( 0.2500000 0.2500000 0.2500000 ) + + number of k points= 29 + cart. coord. in units 2pi/alat + k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 0.0039062 + k( 2) = ( -0.1250000 0.1250000 -0.1250000), wk = 0.0312500 + k( 3) = ( -0.2500000 0.2500000 -0.2500000), wk = 0.0312500 + k( 4) = ( -0.3750000 0.3750000 -0.3750000), wk = 0.0312500 + k( 5) = ( 0.5000000 -0.5000000 0.5000000), wk = 0.0156250 + k( 6) = ( 0.0000000 0.2500000 0.0000000), wk = 0.0234375 + k( 7) = ( -0.1250000 0.3750000 -0.1250000), wk = 0.0937500 + k( 8) = ( -0.2500000 0.5000000 -0.2500000), wk = 0.0937500 + k( 9) = ( 0.6250000 -0.3750000 0.6250000), wk = 0.0937500 + k( 10) = ( 0.5000000 -0.2500000 0.5000000), wk = 0.0937500 + k( 11) = ( 0.3750000 -0.1250000 0.3750000), wk = 0.0937500 + k( 12) = ( 0.2500000 0.0000000 0.2500000), wk = 0.0468750 + k( 13) = ( 0.0000000 0.5000000 0.0000000), wk = 0.0234375 + k( 14) = ( -0.1250000 0.6250000 -0.1250000), wk = 0.0937500 + k( 15) = ( 0.7500000 -0.2500000 0.7500000), wk = 0.0937500 + k( 16) = ( 0.6250000 -0.1250000 0.6250000), wk = 0.0937500 + k( 17) = ( 0.5000000 0.0000000 0.5000000), wk = 0.0468750 + k( 18) = ( 0.0000000 0.7500000 0.0000000), wk = 0.0234375 + k( 19) = ( 0.8750000 -0.1250000 0.8750000), wk = 0.0937500 + k( 20) = ( 0.7500000 0.0000000 0.7500000), wk = 0.0468750 + k( 21) = ( 0.0000000 -1.0000000 0.0000000), wk = 0.0117188 + k( 22) = ( -0.2500000 0.5000000 0.0000000), wk = 0.0937500 + k( 23) = ( 0.6250000 -0.3750000 0.8750000), wk = 0.1875000 + k( 24) = ( 0.5000000 -0.2500000 0.7500000), wk = 0.0937500 + k( 25) = ( 0.7500000 -0.2500000 1.0000000), wk = 0.0937500 + k( 26) = ( 0.6250000 -0.1250000 0.8750000), wk = 0.1875000 + k( 27) = ( 0.5000000 0.0000000 0.7500000), wk = 0.0937500 + k( 28) = ( -0.2500000 -1.0000000 0.0000000), wk = 0.0468750 + k( 29) = ( -0.5000000 -1.0000000 0.0000000), wk = 0.0234375 + + Dense grid: 35749 G-vectors FFT dimensions: ( 45, 45, 45) + + Estimated max dynamical RAM per process > 1.29MB + + Estimated total allocated dynamical RAM > 31.06MB + + Initial potential from superposition of free atoms + + starting charge 7.99901, renormalised to 8.00000 + Starting wfc are 8 randomized atomic wfcs + + total cpu time spent up to now is 0.4 secs + + per-process dynamical memory: 2.9 Mb + + Self-consistent Calculation + + iteration # 1 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.00E-02, avg # of iterations = 2.0 + + Threshold (ethr) on eigenvalues was too large: + Diagonalizing with lowered threshold + + Davidson diagonalization with overlap + ethr = 7.97E-04, avg # of iterations = 1.0 + + total cpu time spent up to now is 0.6 secs + + total energy = -15.84982619 Ry + Harris-Foulkes estimate = -15.87079416 Ry + estimated scf accuracy < 0.06161703 Ry + + iteration # 2 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 7.70E-04, avg # of iterations = 1.0 + + total cpu time spent up to now is 0.7 secs + + total energy = -15.85288351 Ry + Harris-Foulkes estimate = -15.85318795 Ry + estimated scf accuracy < 0.00216687 Ry + + iteration # 3 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 2.71E-05, avg # of iterations = 2.4 + + total cpu time spent up to now is 0.8 secs + + total energy = -15.85332918 Ry + Harris-Foulkes estimate = -15.85336185 Ry + estimated scf accuracy < 0.00007437 Ry + + iteration # 4 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 9.30E-07, avg # of iterations = 2.1 + + total cpu time spent up to now is 0.8 secs + + total energy = -15.85334986 Ry + Harris-Foulkes estimate = -15.85335396 Ry + estimated scf accuracy < 0.00000888 Ry + + iteration # 5 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.11E-07, avg # of iterations = 2.1 + + total cpu time spent up to now is 0.9 secs + + total energy = -15.85335134 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 0.00000011 Ry + + iteration # 6 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.35E-09, avg # of iterations = 2.6 + + total cpu time spent up to now is 1.0 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 2.9E-09 Ry + + iteration # 7 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 3.68E-11, avg # of iterations = 2.6 + + total cpu time spent up to now is 1.1 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 2.9E-11 Ry + + iteration # 8 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 3.65E-13, avg # of iterations = 3.3 + + total cpu time spent up to now is 1.2 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 5.4E-12 Ry + + iteration # 9 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.00E-13, avg # of iterations = 1.7 + + total cpu time spent up to now is 1.3 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 1.2E-13 Ry + + iteration # 10 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.00E-13, avg # of iterations = 1.0 + + total cpu time spent up to now is 1.4 secs + + End of self-consistent calculation + + k = 0.0000 0.0000 0.0000 ( 4477 PWs) bands (ev): + + -5.8300 6.2061 6.2061 6.2061 + + k =-0.1250 0.1250-0.1250 ( 4507 PWs) bands (ev): + + -5.6230 4.6051 5.9132 5.9132 + + k =-0.2500 0.2500-0.2500 ( 4510 PWs) bands (ev): + + -5.0182 2.2559 5.4373 5.4373 + + k =-0.3750 0.3750-0.3750 ( 4501 PWs) bands (ev): + + -4.1058 0.2065 5.1074 5.1074 + + k = 0.5000-0.5000 0.5000 ( 4476 PWs) bands (ev): + + -3.4453 -0.8427 4.9947 4.9947 + + k = 0.0000 0.2500 0.0000 ( 4504 PWs) bands (ev): + + -5.5533 4.8935 5.3857 5.3857 + + k =-0.1250 0.3750-0.1250 ( 4517 PWs) bands (ev): + + -5.0777 2.9801 4.8669 4.9518 + + k =-0.2500 0.5000-0.2500 ( 4508 PWs) bands (ev): + + -4.2481 0.8896 4.3532 4.5964 + + k = 0.6250-0.3750 0.6250 ( 4486 PWs) bands (ev): + + -3.3613 -0.6068 3.9003 4.6231 + + k = 0.5000-0.2500 0.5000 ( 4491 PWs) bands (ev): + + -3.6148 -0.2257 3.7125 4.9256 + + k = 0.3750-0.1250 0.3750 ( 4497 PWs) bands (ev): + + -4.5602 1.5598 3.8591 5.4251 + + k = 0.2500 0.0000 0.2500 ( 4477 PWs) bands (ev): + + -5.2819 3.5267 4.5444 5.9125 + + k = 0.0000 0.5000 0.0000 ( 4520 PWs) bands (ev): + + -4.7329 2.7148 4.2862 4.2862 + + k =-0.1250 0.6250-0.1250 ( 4509 PWs) bands (ev): + + -4.0117 1.2745 3.4881 3.9636 + + k = 0.7500-0.2500 0.7500 ( 4482 PWs) bands (ev): + + -3.0647 -0.1975 2.6082 3.9678 + + k = 0.6250-0.1250 0.6250 ( 4477 PWs) bands (ev): + + -2.8512 -0.4657 2.1376 4.2926 + + k = 0.5000 0.0000 0.5000 ( 4489 PWs) bands (ev): + + -3.7521 0.7207 2.3750 4.8614 + + k = 0.0000 0.7500 0.0000 ( 4484 PWs) bands (ev): + + -3.4015 0.4708 3.5586 3.5586 + + k = 0.8750-0.1250 0.8750 ( 4479 PWs) bands (ev): + + -2.4888 -0.6253 2.7002 3.4815 + + k = 0.7500 0.0000 0.7500 ( 4454 PWs) bands (ev): + + -2.0305 -1.0339 1.8049 3.7440 + + k = 0.0000-1.0000 0.0000 ( 4456 PWs) bands (ev): + + -1.6267 -1.6267 3.3090 3.3090 + + k =-0.2500 0.5000 0.0000 ( 4503 PWs) bands (ev): + + -4.4807 1.9234 3.4393 4.7592 + + k = 0.6250-0.3750 0.8750 ( 4489 PWs) bands (ev): + + -3.5748 0.3447 2.8290 4.2439 + + k = 0.5000-0.2500 0.7500 ( 4486 PWs) bands (ev): + + -2.9014 -0.6278 2.7039 4.0076 + + k = 0.7500-0.2500 1.0000 ( 4484 PWs) bands (ev): + + -3.1970 0.2501 2.7770 3.3923 + + k = 0.6250-0.1250 0.8750 ( 4486 PWs) bands (ev): + + -2.3006 -0.7332 2.0576 3.1860 + + k = 0.5000 0.0000 0.7500 ( 4490 PWs) bands (ev): + + -2.6570 -0.3670 1.8851 3.5717 + + k =-0.2500-1.0000 0.0000 ( 4472 PWs) bands (ev): + + -1.5427 -1.5427 2.7194 2.7194 + + k =-0.5000-1.0000 0.0000 ( 4488 PWs) bands (ev): + + -1.4495 -1.4495 2.2655 2.2655 + + highest occupied level (ev): 6.2061 + +! total energy = -15.86335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 4.0E-15 Ry + + The total energy is the sum of the following terms: + + one-electron contribution = 4.76680131 Ry + hartree contribution = 1.08149972 Ry + xc contribution = -4.81476914 Ry + ewald contribution = -16.88688327 Ry + + convergence has been achieved in 10 iterations + + Forces acting on atoms (cartesian axes, Ry/au): + + atom 1 type 1 force = 0.00000000 0.00000000 0.00000000 + atom 2 type 1 force = 0.00000000 0.00000000 -0.00000000 + + Total force = 0.000000 Total SCF correction = 0.000000 + + + Computing stress (Cartesian axis) and pressure + + total stress (Ry/bohr**3) (kbar) P= 0.05 + 0.00000032 -0.00000000 -0.00000000 0.05 -0.00 -0.00 + -0.00000000 0.00000032 0.00000000 -0.00 0.05 0.00 + -0.00000000 0.00000000 0.00000032 -0.00 0.00 0.05 + + + Writing output data file Si.save + + init_run : 0.06s CPU 0.23s WALL ( 1 calls) + electrons : 0.85s CPU 1.01s WALL ( 1 calls) + forces : 0.00s CPU 0.01s WALL ( 1 calls) + stress : 0.02s CPU 0.03s WALL ( 1 calls) + + Called by init_run: + wfcinit : 0.04s CPU 0.11s WALL ( 1 calls) + potinit : 0.00s CPU 0.01s WALL ( 1 calls) + + Called by electrons: + c_bands : 0.73s CPU 0.80s WALL ( 11 calls) + sum_band : 0.11s CPU 0.13s WALL ( 11 calls) + v_of_rho : 0.00s CPU 0.01s WALL ( 11 calls) + mix_rho : 0.00s CPU 0.01s WALL ( 11 calls) + + Called by c_bands: + init_us_2 : 0.01s CPU 0.03s WALL ( 725 calls) + cegterg : 0.69s CPU 0.74s WALL ( 319 calls) + + Called by sum_band: + + Called by *egterg: + h_psi : 0.62s CPU 0.65s WALL ( 980 calls) + g_psi : 0.00s CPU 0.00s WALL ( 632 calls) + cdiaghg : 0.05s CPU 0.10s WALL ( 922 calls) + + Called by h_psi: + h_psi:pot : 0.61s CPU 0.65s WALL ( 980 calls) + h_psi:calbec : 0.03s CPU 0.04s WALL ( 980 calls) + vloc_psi : 0.57s CPU 0.59s WALL ( 980 calls) + add_vuspsi : 0.01s CPU 0.01s WALL ( 980 calls) + + General routines + calbec : 0.03s CPU 0.05s WALL ( 1125 calls) + fft : 0.01s CPU 0.05s WALL ( 50 calls) + fftw : 0.57s CPU 0.64s WALL ( 8656 calls) + davcio : 0.00s CPU 0.06s WALL ( 29 calls) + + Parallel routines + fft_scatter : 0.29s CPU 0.31s WALL ( 8706 calls) + + PWSCF : 1.07s CPU 2.22s WALL + + + This run was terminated on: 19:30: 3 27Sep2017 + +=------------------------------------------------------------------------------= + JOB DONE. +=------------------------------------------------------------------------------= diff --git a/capolanco/test.scf4.in b/capolanco/test.scf4.in new file mode 100644 index 00000000..34dccffe --- /dev/null +++ b/capolanco/test.scf4.in @@ -0,0 +1,30 @@ + &control + calculation='scf', + outdir = '/global/cscratch1/sd/cpolanco/Si/', + prefix='Si', + pseudo_dir = '/global/homes/c/cpolanco/Materials/pseudo/', + restart_mode='from_scratch', + tprnfor= .true., + tstress= .true., + / + &system + ibrav= 2, + celldm(1)= 10.20777693, + nat= 2, + ntyp= 1, + ecutwfc= 100.0 + / + &electrons + mixing_beta= 0.7 + conv_thr= 1.0d-14 + / + +ATOMIC_SPECIES + Si 28.086 Si.pz-vbc.UPF + +ATOMIC_POSITIONS (alat) + Si 0.00 0.00 0.00 + Si 0.25 0.25 0.25 + +K_POINTS (automatic) + 16 16 16 0 0 0 \ No newline at end of file diff --git a/capolanco/test.scf4.out b/capolanco/test.scf4.out new file mode 100644 index 00000000..c777d624 --- /dev/null +++ b/capolanco/test.scf4.out @@ -0,0 +1,437 @@ + + Program PWSCF v.6.1 starts on 27Sep2017 at 19:30: 1 + + 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); + 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 & OpenMP), running on 24 processor cores + Number of MPI processes: 24 + Threads/MPI process: 1 + R & G space division: proc/nbgrp/npool/nimage = 24 + Waiting for input... + Reading input from standard input + + 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 + + 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 59 59 17 1489 1489 232 + Max 60 60 18 1494 1494 235 + Sum 1417 1417 421 35749 35749 5601 + + + + bravais-lattice index = 2 + lattice parameter (alat) = 10.2078 a.u. + unit-cell volume = 265.9093 (a.u.)^3 + number of atoms/cell = 2 + number of atomic types = 1 + number of electrons = 8.00 + number of Kohn-Sham states= 4 + kinetic-energy cutoff = 100.0000 Ry + charge density cutoff = 400.0000 Ry + convergence threshold = 1.0E-14 + mixing beta = 0.7000 + number of iterations used = 8 plain mixing + Exchange-correlation = SLA PZ NOGX NOGC ( 1 1 0 0 0 0) + + celldm(1)= 10.207777 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) = ( -0.500000 0.000000 0.500000 ) + a(2) = ( 0.000000 0.500000 0.500000 ) + a(3) = ( -0.500000 0.500000 0.000000 ) + + reciprocal axes: (cart. coord. in units 2 pi/alat) + b(1) = ( -1.000000 -1.000000 1.000000 ) + b(2) = ( 1.000000 1.000000 1.000000 ) + b(3) = ( -1.000000 1.000000 -1.000000 ) + + + PseudoPot. # 1 for Si read from file: + /global/homes/c/cpolanco/Materials/pseudo/Si.pz-vbc.UPF + MD5 check sum: 6dfa03ddd5817404712e03e4d12deb78 + Pseudo is Norm-conserving, Zval = 4.0 + Generated by new atomic code, or converted to UPF format + Using radial grid of 431 points, 2 beta functions with: + l(1) = 0 + l(2) = 1 + + atomic species valence mass pseudopotential + Si 4.00 28.08600 Si( 1.00) + + 24 Sym. Ops. (no inversion) found + (note: 24 additional sym.ops. were found but ignored + their fractional translations are incommensurate with FFT grid) + + + Cartesian axes + + site n. atom positions (alat units) + 1 Si tau( 1) = ( 0.0000000 0.0000000 0.0000000 ) + 2 Si tau( 2) = ( 0.2500000 0.2500000 0.2500000 ) + + number of k points= 29 + cart. coord. in units 2pi/alat + k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 0.0039062 + k( 2) = ( -0.1250000 0.1250000 -0.1250000), wk = 0.0312500 + k( 3) = ( -0.2500000 0.2500000 -0.2500000), wk = 0.0312500 + k( 4) = ( -0.3750000 0.3750000 -0.3750000), wk = 0.0312500 + k( 5) = ( 0.5000000 -0.5000000 0.5000000), wk = 0.0156250 + k( 6) = ( 0.0000000 0.2500000 0.0000000), wk = 0.0234375 + k( 7) = ( -0.1250000 0.3750000 -0.1250000), wk = 0.0937500 + k( 8) = ( -0.2500000 0.5000000 -0.2500000), wk = 0.0937500 + k( 9) = ( 0.6250000 -0.3750000 0.6250000), wk = 0.0937500 + k( 10) = ( 0.5000000 -0.2500000 0.5000000), wk = 0.0937500 + k( 11) = ( 0.3750000 -0.1250000 0.3750000), wk = 0.0937500 + k( 12) = ( 0.2500000 0.0000000 0.2500000), wk = 0.0468750 + k( 13) = ( 0.0000000 0.5000000 0.0000000), wk = 0.0234375 + k( 14) = ( -0.1250000 0.6250000 -0.1250000), wk = 0.0937500 + k( 15) = ( 0.7500000 -0.2500000 0.7500000), wk = 0.0937500 + k( 16) = ( 0.6250000 -0.1250000 0.6250000), wk = 0.0937500 + k( 17) = ( 0.5000000 0.0000000 0.5000000), wk = 0.0468750 + k( 18) = ( 0.0000000 0.7500000 0.0000000), wk = 0.0234375 + k( 19) = ( 0.8750000 -0.1250000 0.8750000), wk = 0.0937500 + k( 20) = ( 0.7500000 0.0000000 0.7500000), wk = 0.0468750 + k( 21) = ( 0.0000000 -1.0000000 0.0000000), wk = 0.0117188 + k( 22) = ( -0.2500000 0.5000000 0.0000000), wk = 0.0937500 + k( 23) = ( 0.6250000 -0.3750000 0.8750000), wk = 0.1875000 + k( 24) = ( 0.5000000 -0.2500000 0.7500000), wk = 0.0937500 + k( 25) = ( 0.7500000 -0.2500000 1.0000000), wk = 0.0937500 + k( 26) = ( 0.6250000 -0.1250000 0.8750000), wk = 0.1875000 + k( 27) = ( 0.5000000 0.0000000 0.7500000), wk = 0.0937500 + k( 28) = ( -0.2500000 -1.0000000 0.0000000), wk = 0.0468750 + k( 29) = ( -0.5000000 -1.0000000 0.0000000), wk = 0.0234375 + + Dense grid: 35749 G-vectors FFT dimensions: ( 45, 45, 45) + + Estimated max dynamical RAM per process > 1.29MB + + Estimated total allocated dynamical RAM > 31.06MB + + Initial potential from superposition of free atoms + + starting charge 7.99901, renormalised to 8.00000 + Starting wfc are 8 randomized atomic wfcs + + total cpu time spent up to now is 0.4 secs + + per-process dynamical memory: 2.9 Mb + + Self-consistent Calculation + + iteration # 1 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.00E-02, avg # of iterations = 2.0 + + Threshold (ethr) on eigenvalues was too large: + Diagonalizing with lowered threshold + + Davidson diagonalization with overlap + ethr = 7.97E-04, avg # of iterations = 1.0 + + total cpu time spent up to now is 0.6 secs + + total energy = -15.84982619 Ry + Harris-Foulkes estimate = -15.87079416 Ry + estimated scf accuracy < 0.06161703 Ry + + iteration # 2 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 7.70E-04, avg # of iterations = 1.0 + + total cpu time spent up to now is 0.7 secs + + total energy = -15.85288351 Ry + Harris-Foulkes estimate = -15.85318795 Ry + estimated scf accuracy < 0.00216687 Ry + + iteration # 3 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 2.71E-05, avg # of iterations = 2.4 + + total cpu time spent up to now is 0.8 secs + + total energy = -15.85332918 Ry + Harris-Foulkes estimate = -15.85336185 Ry + estimated scf accuracy < 0.00007437 Ry + + iteration # 4 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 9.30E-07, avg # of iterations = 2.1 + + total cpu time spent up to now is 0.8 secs + + total energy = -15.85334986 Ry + Harris-Foulkes estimate = -15.85335396 Ry + estimated scf accuracy < 0.00000888 Ry + + iteration # 5 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.11E-07, avg # of iterations = 2.1 + + total cpu time spent up to now is 0.9 secs + + total energy = -15.85335134 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 0.00000011 Ry + + iteration # 6 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.35E-09, avg # of iterations = 2.6 + + total cpu time spent up to now is 1.0 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 2.9E-09 Ry + + iteration # 7 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 3.68E-11, avg # of iterations = 2.6 + + total cpu time spent up to now is 1.1 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 2.9E-11 Ry + + iteration # 8 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 3.65E-13, avg # of iterations = 3.3 + + total cpu time spent up to now is 1.2 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 5.4E-12 Ry + + iteration # 9 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.00E-13, avg # of iterations = 1.7 + + total cpu time spent up to now is 1.3 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 1.2E-13 Ry + + iteration # 10 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.00E-13, avg # of iterations = 1.0 + + total cpu time spent up to now is 1.4 secs + + End of self-consistent calculation + + k = 0.0000 0.0000 0.0000 ( 4477 PWs) bands (ev): + + -5.8300 6.2061 6.2061 6.2061 + + k =-0.1250 0.1250-0.1250 ( 4507 PWs) bands (ev): + + -5.6230 4.6051 5.9132 5.9132 + + k =-0.2500 0.2500-0.2500 ( 4510 PWs) bands (ev): + + -5.0182 2.2559 5.4373 5.4373 + + k =-0.3750 0.3750-0.3750 ( 4501 PWs) bands (ev): + + -4.1058 0.2065 5.1074 5.1074 + + k = 0.5000-0.5000 0.5000 ( 4476 PWs) bands (ev): + + -3.4453 -0.8427 4.9947 4.9947 + + k = 0.0000 0.2500 0.0000 ( 4504 PWs) bands (ev): + + -5.5533 4.8935 5.3857 5.3857 + + k =-0.1250 0.3750-0.1250 ( 4517 PWs) bands (ev): + + -5.0777 2.9801 4.8669 4.9518 + + k =-0.2500 0.5000-0.2500 ( 4508 PWs) bands (ev): + + -4.2481 0.8896 4.3532 4.5964 + + k = 0.6250-0.3750 0.6250 ( 4486 PWs) bands (ev): + + -3.3613 -0.6068 3.9003 4.6231 + + k = 0.5000-0.2500 0.5000 ( 4491 PWs) bands (ev): + + -3.6148 -0.2257 3.7125 4.9256 + + k = 0.3750-0.1250 0.3750 ( 4497 PWs) bands (ev): + + -4.5602 1.5598 3.8591 5.4251 + + k = 0.2500 0.0000 0.2500 ( 4477 PWs) bands (ev): + + -5.2819 3.5267 4.5444 5.9125 + + k = 0.0000 0.5000 0.0000 ( 4520 PWs) bands (ev): + + -4.7329 2.7148 4.2862 4.2862 + + k =-0.1250 0.6250-0.1250 ( 4509 PWs) bands (ev): + + -4.0117 1.2745 3.4881 3.9636 + + k = 0.7500-0.2500 0.7500 ( 4482 PWs) bands (ev): + + -3.0647 -0.1975 2.6082 3.9678 + + k = 0.6250-0.1250 0.6250 ( 4477 PWs) bands (ev): + + -2.8512 -0.4657 2.1376 4.2926 + + k = 0.5000 0.0000 0.5000 ( 4489 PWs) bands (ev): + + -3.7521 0.7207 2.3750 4.8614 + + k = 0.0000 0.7500 0.0000 ( 4484 PWs) bands (ev): + + -3.4015 0.4708 3.5586 3.5586 + + k = 0.8750-0.1250 0.8750 ( 4479 PWs) bands (ev): + + -2.4888 -0.6253 2.7002 3.4815 + + k = 0.7500 0.0000 0.7500 ( 4454 PWs) bands (ev): + + -2.0305 -1.0339 1.8049 3.7440 + + k = 0.0000-1.0000 0.0000 ( 4456 PWs) bands (ev): + + -1.6267 -1.6267 3.3090 3.3090 + + k =-0.2500 0.5000 0.0000 ( 4503 PWs) bands (ev): + + -4.4807 1.9234 3.4393 4.7592 + + k = 0.6250-0.3750 0.8750 ( 4489 PWs) bands (ev): + + -3.5748 0.3447 2.8290 4.2439 + + k = 0.5000-0.2500 0.7500 ( 4486 PWs) bands (ev): + + -2.9014 -0.6278 2.7039 4.0076 + + k = 0.7500-0.2500 1.0000 ( 4484 PWs) bands (ev): + + -3.1970 0.2501 2.7770 3.3923 + + k = 0.6250-0.1250 0.8750 ( 4486 PWs) bands (ev): + + -2.3006 -0.7332 2.0576 3.1860 + + k = 0.5000 0.0000 0.7500 ( 4490 PWs) bands (ev): + + -2.6570 -0.3670 1.8851 3.5717 + + k =-0.2500-1.0000 0.0000 ( 4472 PWs) bands (ev): + + -1.5427 -1.5427 2.7194 2.7194 + + k =-0.5000-1.0000 0.0000 ( 4488 PWs) bands (ev): + + -1.4495 -1.4495 2.2655 2.2655 + + highest occupied level (ev): 6.2061 + +! total energy = -15.85435138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 4.0E-15 Ry + + The total energy is the sum of the following terms: + + one-electron contribution = 4.76680131 Ry + hartree contribution = 1.08149972 Ry + xc contribution = -4.81476914 Ry + ewald contribution = -16.88688327 Ry + + convergence has been achieved in 10 iterations + + Forces acting on atoms (cartesian axes, Ry/au): + + atom 1 type 1 force = 0.00000000 0.00000000 0.00000000 + atom 2 type 1 force = 0.00000000 0.00000000 -0.00000000 + + Total force = 0.000000 Total SCF correction = 0.000000 + + + Computing stress (Cartesian axis) and pressure + + total stress (Ry/bohr**3) (kbar) P= 0.05 + 0.00000032 -0.00000000 -0.00000000 0.05 -0.00 -0.00 + -0.00000000 0.00000032 0.00000000 -0.00 0.05 0.00 + -0.00000000 0.00000000 0.00000032 -0.00 0.00 0.05 + + + Writing output data file Si.save + + init_run : 0.06s CPU 0.23s WALL ( 1 calls) + electrons : 0.85s CPU 1.01s WALL ( 1 calls) + forces : 0.00s CPU 0.01s WALL ( 1 calls) + stress : 0.02s CPU 0.03s WALL ( 1 calls) + + Called by init_run: + wfcinit : 0.04s CPU 0.11s WALL ( 1 calls) + potinit : 0.00s CPU 0.01s WALL ( 1 calls) + + Called by electrons: + c_bands : 0.73s CPU 0.80s WALL ( 11 calls) + sum_band : 0.11s CPU 0.13s WALL ( 11 calls) + v_of_rho : 0.00s CPU 0.01s WALL ( 11 calls) + mix_rho : 0.00s CPU 0.01s WALL ( 11 calls) + + Called by c_bands: + init_us_2 : 0.01s CPU 0.03s WALL ( 725 calls) + cegterg : 0.69s CPU 0.74s WALL ( 319 calls) + + Called by sum_band: + + Called by *egterg: + h_psi : 0.62s CPU 0.65s WALL ( 980 calls) + g_psi : 0.00s CPU 0.00s WALL ( 632 calls) + cdiaghg : 0.05s CPU 0.10s WALL ( 922 calls) + + Called by h_psi: + h_psi:pot : 0.61s CPU 0.65s WALL ( 980 calls) + h_psi:calbec : 0.03s CPU 0.04s WALL ( 980 calls) + vloc_psi : 0.57s CPU 0.59s WALL ( 980 calls) + add_vuspsi : 0.01s CPU 0.01s WALL ( 980 calls) + + General routines + calbec : 0.03s CPU 0.05s WALL ( 1125 calls) + fft : 0.01s CPU 0.05s WALL ( 50 calls) + fftw : 0.57s CPU 0.64s WALL ( 8656 calls) + davcio : 0.00s CPU 0.06s WALL ( 29 calls) + + Parallel routines + fft_scatter : 0.29s CPU 0.31s WALL ( 8706 calls) + + PWSCF : 1.07s CPU 2.22s WALL + + + This run was terminated on: 19:30: 3 27Sep2017 + +=------------------------------------------------------------------------------= + JOB DONE. +=------------------------------------------------------------------------------= From 2ab45088289ead2cedbae7ad2d1307454da1b0a6 Mon Sep 17 00:00:00 2001 From: cpolanco Date: Thu, 8 Dec 2022 23:32:57 +0100 Subject: [PATCH 3/3] Added support to send the QE calculations to the cluster. For that created a class to handle cluster jobs. --- capolanco/RunConvergence.py | 41 +++++++++++-- .../__pycache__/ioclusterclass.cpython-39.pyc | Bin 0 -> 1384 bytes capolanco/ioclusterclass.py | 58 ++++++++++++++++++ capolanco/job.test.sh | 12 ++++ capolanco/job.test1.sh | 12 ++++ capolanco/job.test2.sh | 12 ++++ capolanco/job.test3.sh | 12 ++++ capolanco/job.test4.sh | 12 ++++ 8 files changed, 155 insertions(+), 4 deletions(-) create mode 100644 capolanco/__pycache__/ioclusterclass.cpython-39.pyc create mode 100644 capolanco/ioclusterclass.py create mode 100644 capolanco/job.test.sh create mode 100644 capolanco/job.test1.sh create mode 100644 capolanco/job.test2.sh create mode 100644 capolanco/job.test3.sh create mode 100644 capolanco/job.test4.sh diff --git a/capolanco/RunConvergence.py b/capolanco/RunConvergence.py index b78b0abd..892ecf6c 100644 --- a/capolanco/RunConvergence.py +++ b/capolanco/RunConvergence.py @@ -1,7 +1,8 @@ # This code will run a k-point convergence up to a desire delta energy - +import subprocess import ioqeclass as qe +import ioclusterclass as cluster ########################### ##### USER INPUTS @@ -21,11 +22,24 @@ ##### DEVELOPERS INPUTS ########################### +## Convergence # maximum of iterations Nitermax=20 # increasing step of kgrid kstep=2 +## Cluster +# number of nodes to be used +Nnodes=1 +# number of processors per node +ppn=8 +# queue +queue='OR' +# walltime +walltimehours=5 +walltimeminutes=3 + + ########################### ##### PROGRAM ########################### @@ -40,8 +54,23 @@ testin='test.scf.in' testout='test.scf.out' qeinput.save(filein,testin) +# Create the job to send to the cluster +# Initialize job class +job=cluster.jobclass() +# set up job class +job.name='test' +job.nodes=Nnodes +job.ppn=ppn +job.queue=queue +job.walltimehours=walltimehours +job.walltimeminutes=walltimeminutes +# create the job file +jobname=f'job.test.sh' +job.createjobQEpw(jobname,testin,testout) # Run initial test -##### pw.x test.scf.in test.scf.out +subprocess.run(['echo',f'runing {jobname}']) +##subprocess.run(['qsub',f'{jobname}']) + # Initialize pw.x output class qeoutput=qe.qepwoutput() # Read the Total energy from the output @@ -66,8 +95,12 @@ testout=f'test.scf{counter}.out' qeinput.save(filein,testin) - # Run initial test - ##### pw.x test.scf{counter}.in test.scf{counter}.out + # create the job file + jobname=f'job.test{counter}.sh' + job.createjobQEpw(jobname,testin,testout) + # Run QE calculation + subprocess.run(['echo',f'runing {jobname}']) + ##subprocess.run(['qsub',f'{jobname}']) # Read the Total energy from the output qeoutput.getenergy(testout) diff --git a/capolanco/__pycache__/ioclusterclass.cpython-39.pyc b/capolanco/__pycache__/ioclusterclass.cpython-39.pyc new file mode 100644 index 0000000000000000000000000000000000000000..12df40cf06d5a2fa7cc660073dcbf438be63afac GIT binary patch literal 1384 zcmZ`(&2Qv16t|OjCQWDh#V%SvLPoO^n!|P~K&#b?qQVv-K$>0lLrA%pGD8}C*?s5Mu;{Lf8dmO(&XV_z?UQE5&La~IN$*% zZ&6Hm52EyKcq)(5JTa#J^yNurXhYLfi=-5Wg3{1qscCs4KvkJi=oCZbZaCU)`3X#O z0KoAAF;wC|JnmgN+Fzjq?t_G^NO}z&G?smiU`u2glUIciZSTorfK zYa23_6U3lHMGw`h0N*{)q73{4KFerIY?{lVz}M!hu}(I>7cv*K6R zmDJ*SJsf>9Im(L3QDRP_s18TZzIj0(OhFgb8!eO5rb+heLB~V4?02STv|exJr&Nll z-tLULzS)ocz0deHeq58sdwY;$C*|}$q+w6l&rhHKc=-MEsJ=Usyvha5Wx}a2N(*CT zRNtGaOjiYcP^i{r`i!di?r-!O({W^p($K~>kV-)N&UFS?%bmRr9jrNUFNI!r;F`#i zG?zwzM_n`{zM#OzJ&k9wQaj539DuJ^2xasc}Hl6RVz0u(F)3<8=F^G%<)C+Nl zH~h$t@SU44!qkg!gztIv`^#4SkNb4ob4~8DGiD>k+5!MQVC<|)@*7Q`F)mZa^cG~& zA31Q>ZUx-lw0pAPDMZFWhyxPtG_tV|SG=03*V-u>(TZymsrk3?%QpX4?x8R)T1fr@ D1M5>| literal 0 HcmV?d00001 diff --git a/capolanco/ioclusterclass.py b/capolanco/ioclusterclass.py new file mode 100644 index 00000000..ea4e0716 --- /dev/null +++ b/capolanco/ioclusterclass.py @@ -0,0 +1,58 @@ +import numpy as np + + +## THINGS TO FIX + +class jobclass: + """This class creates jobs for the cluster""" + + ################### + ## Initialization function for the class + ################### + def __init__(self): + + ## name of the job + self.name='Unset' + ## number of nodes + self.nodes=np.int64(1) + ## number of processors per node + self.ppn=np.int64(1) + ## queue + self.queue='D' + ## walltime (in hours) + self.walltimehours=np.int64(1) + self.walltimeminutes=np.int64(0) + + + ################### + ## Create the job for QE pw.x calculation + ################### + def createjobQEpw(self,jobname,pwinput,pwoutput): + # Inputs + # jobname is the name of the job + # pwinput is the path of the input file + # pwoutput is the path of the output file + + print('') + print(f'#########################') + print(f'## Creating job {jobname}') + + # Open file + f=open(jobname,'w') + + # Write heather of job + f.write(f'#!/bin/bash\n\n') + f.write(f'#PBS -N {self.name}\n') + f.write(f'#PBS -l nodes={self.nodes}\n') + f.write(f'#PBS -l ppn={self.ppn}\n') + f.write(f'#PBS -q {self.queue}\n') + f.write(f'#PBS -j oe\n') + f.write(f'#PBS -l walltime={self.walltimehours:02d}:{self.walltimeminutes:02d}:00\n\n') + + f.write(f'cd $PBS_O_WORKDIR\n') + f.write(f'module load espresso\n') + f.write(f'mpirun -np $PBS_NP pw.x {pwinput} {pwoutput}\n') + + f.close() + + diff --git a/capolanco/job.test.sh b/capolanco/job.test.sh new file mode 100644 index 00000000..ddcc703e --- /dev/null +++ b/capolanco/job.test.sh @@ -0,0 +1,12 @@ +#!/bin/bash + +#PBS -N test +#PBS -l nodes=1 +#PBS -l ppn=8 +#PBS -q OR +#PBS -j oe +#PBS -l walltime=05:03:00 + +cd $PBS_O_WORKDIR +module load espresso +mpirun -np $PBS_NP pw.x test.scf.in test.scf.out diff --git a/capolanco/job.test1.sh b/capolanco/job.test1.sh new file mode 100644 index 00000000..9ce1cf81 --- /dev/null +++ b/capolanco/job.test1.sh @@ -0,0 +1,12 @@ +#!/bin/bash + +#PBS -N test +#PBS -l nodes=1 +#PBS -l ppn=8 +#PBS -q OR +#PBS -j oe +#PBS -l walltime=05:03:00 + +cd $PBS_O_WORKDIR +module load espresso +mpirun -np $PBS_NP pw.x test.scf1.in test.scf1.out diff --git a/capolanco/job.test2.sh b/capolanco/job.test2.sh new file mode 100644 index 00000000..1b628d2c --- /dev/null +++ b/capolanco/job.test2.sh @@ -0,0 +1,12 @@ +#!/bin/bash + +#PBS -N test +#PBS -l nodes=1 +#PBS -l ppn=8 +#PBS -q OR +#PBS -j oe +#PBS -l walltime=05:03:00 + +cd $PBS_O_WORKDIR +module load espresso +mpirun -np $PBS_NP pw.x test.scf2.in test.scf2.out diff --git a/capolanco/job.test3.sh b/capolanco/job.test3.sh new file mode 100644 index 00000000..33c390a3 --- /dev/null +++ b/capolanco/job.test3.sh @@ -0,0 +1,12 @@ +#!/bin/bash + +#PBS -N test +#PBS -l nodes=1 +#PBS -l ppn=8 +#PBS -q OR +#PBS -j oe +#PBS -l walltime=05:03:00 + +cd $PBS_O_WORKDIR +module load espresso +mpirun -np $PBS_NP pw.x test.scf3.in test.scf3.out diff --git a/capolanco/job.test4.sh b/capolanco/job.test4.sh new file mode 100644 index 00000000..26d9d500 --- /dev/null +++ b/capolanco/job.test4.sh @@ -0,0 +1,12 @@ +#!/bin/bash + +#PBS -N test +#PBS -l nodes=1 +#PBS -l ppn=8 +#PBS -q OR +#PBS -j oe +#PBS -l walltime=05:03:00 + +cd $PBS_O_WORKDIR +module load espresso +mpirun -np $PBS_NP pw.x test.scf4.in test.scf4.out