From 2e296b499767a4bd864e1fadec35f3bca59bda93 Mon Sep 17 00:00:00 2001 From: Aditya Wibawa Sakti Date: Sun, 16 Apr 2023 09:36:16 +0900 Subject: [PATCH] Modified DCDFTBMD --- bin/cmmde.py | 33 ++++++++++++------ lib/__pycache__/cmmde_msd_com.cpython-310.pyc | Bin 0 -> 5870 bytes lib/__pycache__/cmmde_rdf.cpython-310.pyc | Bin 0 -> 2285 bytes 3 files changed, 23 insertions(+), 10 deletions(-) create mode 100644 lib/__pycache__/cmmde_msd_com.cpython-310.pyc create mode 100644 lib/__pycache__/cmmde_rdf.cpython-310.pyc diff --git a/bin/cmmde.py b/bin/cmmde.py index 4eb17b2..2d059b8 100755 --- a/bin/cmmde.py +++ b/bin/cmmde.py @@ -449,19 +449,32 @@ mpirun -np {} $QE_COMMAND < cmmd.in > cmmd.out""".format(opt.nproc,opt.nproc),fi os.system('sbatch run.sh') if opt.software == 'dcdftb': - os.system("cp cmmd.in dftb.inp") - with open('run.sh','w') as fout: - print("""#!/bin/bash -#SBATCH --nodes=1 -#SBATCH --ntasks=1 -#SBATCH --cpus-per-task=1 -#SBATCH --time=168:0:0 -export OMP_NUM_THREADS={} + if opt.slurm == 'true': + os.system("cp cmmd.in dftb.inp") + with open('run.sh','w') as fout: + print("""#!/bin/bash + #SBATCH --nodes=1 + #SBATCH --ntasks=1 + #SBATCH --cpus-per-task=1 + #SBATCH --time=168:0:0 + export OMP_NUM_THREADS={} + cd $PWD + $DCDFTB_COMMAND + mv dftb.out cmmd.out + mv traject traject.xyz""".format(opt.nproc),file=fout) + os.system('sbatch run.sh') + else: + os.system("cp cmmd.in dftb.inp") + with open('run.sh','w') as fout: + print("""#!/bin/bash cd $PWD $DCDFTB_COMMAND mv dftb.out cmmd.out -mv traject traject.xyz""".format(opt.nproc),file=fout) - os.system('sbatch run.sh') +if [-f traject.xyz]; then +mv traject traject.xyz +fi""",file=fout) + os.system("chmod +x run.sh") + os.system('./run.sh') if opt.software == 'gromacs': if opt.slurm == 'true': diff --git a/lib/__pycache__/cmmde_msd_com.cpython-310.pyc b/lib/__pycache__/cmmde_msd_com.cpython-310.pyc new file mode 100644 index 0000000000000000000000000000000000000000..e7b905e9d3d2b71ab96250426e0a87bf6fcabdda GIT binary patch literal 5870 zcmb_g&669)b)TLOU@!|{vAfvs56+UbM66c(L5Y&QVpvi|cEyoIDPG!g#-dR}^k6x= zg8{Z@U~<78$H~fxR52|&Cm(XarYZ;Jl#BlZSMmqsHpiqYRji~cl}c3(I)wSX8GuV# za!wi4On<$8{od=>{eBPKO2ty}?Emd1*VYx~U#RiyqoMH@-sng8aD}r#aq^NmD%xtG zb#zDX7>>d6{z9kdn4@~hDS4%##kDgw>Y3=2oeJtYH$G9EDlhON%1O@lm4^8kYbZAx zYFZ53IQCm!T8d)PZ^eD#rRsZq;)%E{ zCx^%Nj>*^&*p`IO7%;jG-6SLzD%YRHZA5wtg8>%Rl_#wv}GbdBtsy-41}jd|rW+Kmog zk1UgE@!z0Zgzv75%2mF0z@X=9wij#RpTbhxcz5C@xguBPWw~~$L)w=<)|1`jYVu0* zDr`_0F3YR(l{1yBm0Xjr%4_pV@*0gCF3Vl{ihPYahydRAGWdl<@fityJCGN!gL8 zP$zx9+}QqJvnD@+l8U**yrw%ebfyjtmTDU zgVMWRfF-*}dxQ7Jmff=-B%9Ao8!eFA_qpNGDt1nhaqSR6s@!Uk2IGhD0of@t>;RRR zq6EAScaNIa5)G$9$7{fE5yx;UE+mD~7)4->;*ivbIwA+QAv+qc5L2{Ox%ONP zoQ}=Il2oKF4MGYJ^#rjF+g7-lc}Ko^6#Q>BbV0(V#i-}Cd@o81t!`KF$f@UL(-mH` z<%-ygd^c=Zspf}qs)yeFI5mVD9(bt{^#VUm3vRE6eMoiM%v9^Rz0_z2T{jlw{%L7{ zj6@n%z9eg>TIhmJ?8kv8WtV_52j(4RO zHSFik2%Vg#XM`5b&PWkq5?h&QlI5r4Tv%AQ3NkTCp9}b;M))=Ah$#%U@Mf+*r!-iq zxBb9-ZgJWs5`gR!k)5)|3kmxahjV^(FrQgk&6ZBt{V$kf(Gh6+I3@RU3Nm80DmmnT z5$n1#n4lZQZ`rt@qK1}x%F`RA!JNXO-*FGTf%RbT`tHuwwRU0;N)Ps~?riN|Z6^m{ z0<8P_TZ7sy_paN+QLrN~@FLf5tcnGUrCQ*HsnHYULWQ0ya6_b4)@865UJ7j1$dRSVq_I@nMU+BPKRUV#%m&zK%Hpm-j1A7fGCw$Co)4dsRJ6s zI6D!JZN#yexNCc9AR+z!bwq*6mnyGDd^t?8?s@kzPC!NuKIxZhSQ-xr$x%qoz~H<-sKsai^L$T78ilt@Km}#~iER6loaj9qU{br}A{B zz^*tWEfK8UzyTK&A-kLhis%kmoVX>8epI)%&@>8p9 z4yCT?%+##OGFwwee8IhnSH%igd$g7bK1*sgu)(lC58fGkk z#svQ=embPl)fy=4ps%ruY+9{B9`mQ_6a636z01E5A3)U>-T&iUk`c-6v z`Uo$Y7|D8)3B*n<){$`mTjqHp@>DI0pVT{=G0q`nfiv*?9%3tHbNYgk6u^sO?Wm0$ z*o~3pQqFW-e-;mB8E5b;7DPT&99puFBh9#UN?B-$a%q%^-lt3!!0%U?))Nvup>6py zMVdp6n?vhUXf%(QPf`E)FXJ)APd)<|j(-Qn;~Bs5VMXe3`LN2Zhw2dj3vm5RP0F$? 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