How to use test_job_log method in avocado

Best Python code snippet using avocado_python

relax.py

Source:relax.py

1#!/usr/local/bin/python3.82"""relax.py3This test code gets Relax density matrix (1-body) by computing 4expectation values of perturbed Hamiltonians.5This program relies on the Quket log format where6the final converged energy appears as7Final: E[uccsd] = -7.882391426828  ... 8                  ~~~~~~~~~~~~~~~9                  10It also requires a modified version of PySCF 11(installed only on Ravel) to add perturbation 12to a certain one-body term in the atomic orbital basis. 13HOW TO USE:14    Simply run this code with a Quket input.15        e.g.)   python3.8 relax.py uccsd_LiH > rdm &16    Then, this program will create ***_dm.inp file and 17    submit to perform several jobs. Computing NBasis*(NBasis+1)/218    jobs may take some time, but if you already have ***_dm.log 19    finished in your directory, you can bypass the re-calculation20    by setting the option "bypass".21"""22### CHANGE ACCORDINGLY ###23delta = 0.000000124nprocs = 2825nthread = 226QDIR = "/home/tsuchimochi/Quket/master"27bypass = False28### YOU MAY MODIFY BELOW TO GET WHAT YOU WANT ###29import os30import re31import sys32import time33import sh34import glob35import numpy as np36np.set_printoptions(precision=10, suppress=True)37np.set_printoptions(threshold=np.inf)38np.set_printoptions(linewidth=2000)39def Submit(jobname, nprocs=1, nthread=1):40    """Function41    Submit job. Track the submitted job until its finished.42    """43    job = '.job'44    job_script = f"{input_dir}/{jobname+job}"45    ### Make job script46    with open(job_script, "w") as f:47        print("#!/bin/bash", file=f)48        print("#PBS -N ", jobname, file=f)49        print("#PBS -l select=1:ncpus={}:mpiprocs={}".format(nprocs, nprocs), file=f)50        print("", file=f)51        print("cd ${PBS_O_WORKDIR}", file=f)52        print("", file=f)53        print("export OMP_NUM_THREADS={}".format(nthread), file=f)54        print("mpirun -np {} -genv I_MPI_FABRICS tcp /usr/local/bin/python3.8 -m mpi4py {}/main.py {} -nt {}".format(nprocs, QDIR, jobname, nthread), file=f)55    56    57    sh.chmod("755", job_script)58    job_id = sh.qsub(job_script)59    job_id = job_id.strip()60    61    qstat = True62    test = 063    while qstat:64        log = sh.qstat().split()65        if job_id not in log:66            # Job done67            qstat = False68        time.sleep(1)69def ReadMatrix(NDim, Mat_name, filename):70    """Function71    Get Matrix(NDim, NDim) from file.72    """73    Nlines = ((NDim//10) + 1) * (NDim + 2)74    log = str(sh.grep("-A", Nlines, Mat_name, filename)).split("\n")75    Mat = np.zeros((NDim, NDim), dtype=float)76    77    for p in range(NDim):78        for qq in range(NDim//10):79            row = (NDim+2)*qq + 380            log_line = log[p+row].split()81            for q in range(10):82    #            print(log_line)83    #            print('({}, {}) = {}'.format(p,qq*10+q,log_line[q+1]))84                Mat[p, qq*10 + q] = float(log_line[q+1])85        qq = NDim//10       86        row = (NDim+2)*qq + 387        log_line = log[p+row].split()88        for q in range(NDim%10):89            #print(log_line)90    #        print('({}, {}) = {}'.format(p,q+qq*10,log_line[q+1]))91            Mat[p, qq*10 + q] = float(log_line[q+1])92    return Mat    93################################################################94#                   Setting for input and output               #95################################################################96len_argv = len(sys.argv)97if len_argv == 1:98    print("Error! No input loaded.")99    exit()100# First argument = Input file,  either "***.inp" or "***" is allowed.101input_file=sys.argv[1]102input_dir, base_name = os.path.split(input_file)103input_dir = "." if input_dir == "" else input_dir104input_name, ext = os.path.splitext(base_name)105if ext == "":106    ext = ".inp"107elif ext not in ".inp":108    input_name += ext109    ext = ".inp"110input_file = f"{input_dir}/{input_name+ext}"111test = "_test"112dm = "_dm"113tmp = "tmpfile"114job = ".job"115log = ".log"116test_job = f"{input_name+test}" 117dm_job = f"{input_name+dm}"118dm_job_path = f"{input_dir}/{input_name+dm+ext}"119dm_job_log = f"{input_dir}/{input_name+dm+log}"120test_job_path = f"{input_dir}/{test_job+ext}"121test_job_log = f"{input_dir}/{test_job+log}"122tmpfile = f"{input_dir}/{tmp}"123try:124    if sys.argv[2] == 'bypass' and os.path.isfile(test_job_log):125        bypass = True126except:127    bypass = False128# Prepare input files and run calculations... 129### Get Input file130num_lines = sum(131    1 for line in open(input_file)132)  # number of lines in the input file133f = open(input_file)134lines = f.readlines()135if bypass:136    pass137else:138    print('Running test job to get NBasis')139    with open(test_job_path, "w") as f:140        for i in lines:141            print(i.replace('\n',''), file=f)142        print('MaxIter = 0', file=f)143        print('debug = True', file=f)144        #print('pyscf_guess = minao', file=f)145        print('pyscf_guess = read', file=f)146        print('theta_guess = zero', file=f)147        print('kappa_guess = zero', file=f)148    Submit(test_job, nprocs=nprocs, nthread=nthread)149    print('Test job Done')150### Open test.log and get NBasis151num_lines = sum(152    1 for line in open(test_job_log)153)  # number of lines in the input file154f = open(test_job_log)155test_lines = f.readlines()156iline = 0157NBasis = None158nf = None159nc = None160nact = None161while iline < num_lines or NBasis is None or nf is None or nc is None or nact is None:162    line = test_lines[iline].replace("=", " ")163    print(line)164    words = [x.strip() for x in line.split() if not line.strip() == ""]165    print('word ',words)166    len_words = len(words)167    if len_words > 0 and words[0][0] not in {"!", "#"}:168        if words[0].lower() == "nbasis":169            NBasis = int(words[1])170        elif words[0].lower() == "n_frozen_orbitals":171            nf = int(words[1])172        elif words[0].lower() == "n_core_orbitals":173            nc = int(words[1])174        elif words[0].lower() == "n_active_orbitals":175            nact = int(words[1])176    iline += 1177### Get MO_coeff and Overlap matrices178MO_coeff = ReadMatrix(NBasis, "MO coeff", test_job_log)179Overlap = ReadMatrix(NBasis, "Overlap", test_job_log)180print("MO_coeff = \n",MO_coeff)181print("Overlap = \n",Overlap)182MO_coeff_act = MO_coeff[:,(nf+nc):(nf+nc+nact)] 183print("MO_coeff = \n",MO_coeff_act)184#Delete files...185wildcard = "*"186sh.cp(test_job_log, tmpfile) 187sh.rm(sh.glob(f"{test_job+wildcard}"))188sh.cp(tmpfile, test_job_log) 189sh.rm(sh.glob(tmpfile))190print("NBasis = ",NBasis)191print('Creating {}'.format(dm_job_path))192if bypass:193    print(f"Will bypass computing {dm_job}")194else:195    pq = 0196    for p in range(NBasis):197        for q in range(p+1):198            for s in range(2):199                if s == 0:200                    sign = '+'201                else:202                    sign = '-'203                str_pq = str(pq)204                dm_job = f"{input_name+dm+sign+str_pq}"205                dm_job_path = f"{input_dir}/{input_name+dm+sign+str_pq+ext}"206                with open(dm_job_path, "w") as f:207                    for i in lines:208                        print(i.replace('\n',''), file=f)209                    print('theta_guess = zero', file=f)210                    print('kappa_guess = zero', file=f)211                    print('IntPQ = 0 0 ', delta, file=f)212                    print('debug = False', file=f)213                    print('1RDM = False', file=f)214                    print('ftol = 1e-14', file=f)215                    print('gtol = 1e-6', file=f)216                    if sign == '+':217                        print('IntPQ = {} {} {} '.format(p, q, delta), file=f)218                    elif sign == '-':219                        print('IntPQ = {} {} {} '.format(p, q, -delta), file=f)220               221                Submit(dm_job, nprocs=nprocs)222                dm_job_log = f"{input_dir}/{input_name+dm+sign+str_pq+log}"223                sh.cp(dm_job_log, tmpfile) 224                sh.rm(sh.glob(f"{dm_job+wildcard}"))225                sh.cp(tmpfile, dm_job_log) 226                sh.rm(sh.glob(tmpfile))227            pq += 1228    print('end of job: now compute relax density matrix')229DM_AO = np.zeros((NBasis, NBasis), dtype=float)230pq = 0231for p in range(NBasis):232    for q in range(p+1):233        str_pq = str(pq)234        dm_job_log = f"{input_name+dm+'+'+str_pq+log}"235        final = str(sh.grep("Final:", dm_job_log)).split("\n")236        Ep = float(final[0].split()[3])237        dm_job_log = f"{input_name+dm+'-'+str_pq+log}"238        final = str(sh.grep("Final:", dm_job_log)).split("\n")239        Em = float(final[0].split()[3])240        print(f"{p} {q}  {Ep}  {Em}")241        DM_AO[p,q] = (Ep - Em) / (4*delta)242        DM_AO[q,p] = DM_AO[p,q]243        pq += 1244print("Relaxed DM in AO (alpha+beta) \n",DM_AO)245### Compute DM in MO 246DM_MO_act =  MO_coeff_act.T @ Overlap @ DM_AO @ Overlap @ MO_coeff_act247print("Relaxed DM in MO (alpha+beta): active\n",DM_MO_act)248print("Relaxed DM in MO alpha: active\n",DM_MO_act/2)249### Compute DM in MO 250DM_MO =  MO_coeff.T @ Overlap @ DM_AO @ Overlap @ MO_coeff251print("Relaxed DM in MO (alpha+beta): whole\n",DM_MO)...

test_scrapydApi.py

Source:test_scrapydApi.py

...31    def test_logs(self):32        print(self.api.logs())33    def test_spider_logs(self):34        print(self.api.spider_logs(self.project, 'baidu'))35    def test_job_log(self):...

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