From 50197aaf021efe044a44d41c5e1593c68c4770c2 Mon Sep 17 00:00:00 2001
From: Aditya Wibawa Sakti <adit@Adityas-MacBook-Pro-2.local>
Date: Fri, 1 Dec 2023 16:10:57 +0900
Subject: [PATCH] fix bug with the temperature in -s gromacs

---
 bin/cmmde.py                              |   4 ++--
 lib/__pycache__/cmmde_rdf.cpython-310.pyc | Bin 2285 -> 2286 bytes
 lib/cmmde_rdf.py                          |   5 +++--
 3 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/bin/cmmde.py b/bin/cmmde.py
index 91b7adc..817ebd4 100755
--- a/bin/cmmde.py
+++ b/bin/cmmde.py
@@ -487,14 +487,14 @@ if opt.software == 'gromacs':
 #SBATCH --time=168:0:0
 export OMP_NUM_THREADS=1
 cd $PWD
-$GROMACS_COMMAND -mt {} -mp {} -ct {} -pt {} -pp {} -l {} -cat {} -gen {} -Nump {} -prod {} -nprod {} -nequil {} -dt {} -ctype  {} -nnpt {} -comp {} -np {}""".format(opt.terlarut,opt.pelarut,opt.c_terlarut,opt.persen_terlarut,opt.persen_pelarut,opt.lapang,opt.cation,opt.generate_dftbinp,opt.NumPelarut,opt.production,opt.nprod,opt.nequil,opt.deltat,opt.charge_type,opt.nnpt,opt.compress,opt.nproc,opt.rcol),file=fout)
+$GROMACS_COMMAND -mt {} -mp {} -ct {} -pt {} -pp {} -l {} -cat {} -gen {} -Nump {} -prod {} -nprod {} -nequil {} -dt {} -ctype  {} -nnpt {} -comp {} -np {} -rc {} -t {}""".format(opt.terlarut,opt.pelarut,opt.c_terlarut,opt.persen_terlarut,opt.persen_pelarut,opt.lapang,opt.cation,opt.generate_dftbinp,opt.NumPelarut,opt.production,opt.nprod,opt.nequil,opt.deltat,opt.charge_type,opt.nnpt,opt.compress,opt.nproc,opt.rcol,opt.temp),file=fout)
 		os.system('sbatch run.sh')
 	else:
 		with open('run.sh','w') as fout:
 			print("""#!/bin/bash
 export OMP_NUM_THREADS=1
 cd $PWD
-$GROMACS_COMMAND -mt {} -mp {} -ct {} -pt {} -pp {} -l {} -cat {} -gen {} -Nump {} -prod {} -nprod {} -nequil {} -dt {} -ctype  {} -nnpt {} -comp {} -np {}""".format(opt.terlarut,opt.pelarut,opt.c_terlarut,opt.persen_terlarut,opt.persen_pelarut,opt.lapang,opt.cation,opt.generate_dftbinp,opt.NumPelarut,opt.production,opt.nprod,opt.nequil,opt.deltat,opt.charge_type,opt.nnpt,opt.compress,opt.nproc,opt.rcol),file=fout)
+$GROMACS_COMMAND -mt {} -mp {} -ct {} -pt {} -pp {} -l {} -cat {} -gen {} -Nump {} -prod {} -nprod {} -nequil {} -dt {} -ctype  {} -nnpt {} -comp {} -np {} -rc {} -t {}""".format(opt.terlarut,opt.pelarut,opt.c_terlarut,opt.persen_terlarut,opt.persen_pelarut,opt.lapang,opt.cation,opt.generate_dftbinp,opt.NumPelarut,opt.production,opt.nprod,opt.nequil,opt.deltat,opt.charge_type,opt.nnpt,opt.compress,opt.nproc,opt.rcol,opt.temp),file=fout)
 		os.system('chmod +x run.sh')
 		os.system('./run.sh')		
 
diff --git a/lib/__pycache__/cmmde_rdf.cpython-310.pyc b/lib/__pycache__/cmmde_rdf.cpython-310.pyc
index d20cad8c56ea1eefecaaf713a18fee020d83cba1..b3a01cf066196aeaec1a7ea7e10a0a9dca236242 100644
GIT binary patch
delta 583
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za&&kIGl5`!AQ%|>3(O8KFf{NH_yg=YA0XJ!RrFWiSJc<_CHNY+k6qUSb#A`?jvo)*
zH|+W0+v=$%`oa=6nPvZuCLH04L2Z>b0rpT|aN*TX=~AC8vdJNr2D`dK252lec{?6?
zwZ9V}2w&ZRc+*3(Wg@Hr`%Oq8S~;kw<<N4p=UhbOH4!?$Do0Sh;)?G71r_lK&aj}4
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EPe;p+#{d8T

delta 566
zcmZWmy=xRf6n}3vcemdkx4XA@w|CyfO(7(rO%N*!!DwM2+C+py7!z4d!d({9yg}g*
zY>p77RAILe>;qzB>tB)1QnayGXJZt^8TkF){N4xe&HEO74V*p4F+rWXZ`b(iBj+8y
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zKz=@)qvD|E2vQJrkyzegp>a-Gqtn+88*ZM(rf>yBpHi+pVYBbklVZ%HGN1tssb6Un
z@_4}zrY97Z%cpGt?<oI&pK&-4BbA$!f&9$Y<I4w#Y6yhQdX)2J#=B*3d{O(za7BJ;
zth@KyPao}W7mxQR4|n<Gc(u8VIF`3t8D?_Yx`7+=Lu)O|)IRH_?%z|egf{Bxj*&fQ
uKL$U|Mh9Ic4gH$RxuuV>FLQkbQ+cR&M<bOmyHrD6W47@x+?1d63%>v+QHDGK

diff --git a/lib/cmmde_rdf.py b/lib/cmmde_rdf.py
index 50c7804..372e9de 100644
--- a/lib/cmmde_rdf.py
+++ b/lib/cmmde_rdf.py
@@ -15,8 +15,9 @@ def rdf(traject,latt,pair,endrange,resolution):
                 cell.append(list(map(float, line.split()[1:4])))
 
     box = lattice.Lattice(cell)
-    (lx, ly, lz), (a, b, c) = box.lengths_and_angles
-
+    # (lx, ly, lz), (a, b, c) = box.lengths_and_angles
+    lx, ly, lz = box.lengths
+    a, b, c = box.angles
     u = MDAnalysis.Universe(traject, format='XYZ')
     u.dimensions = np.array([lx, ly, lz, a, b, c], dtype=np.float32)