fix bug with the temperature in -s gromacs

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')		
 

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)