initial commit

2025-08-09 13:43:03 +02:00
parent dce92e4a2e
commit b02fe38415
11 changed files with 8629 additions and 0 deletions
--- a/setup_sim.sh
+++ b/setup_sim.sh
@@ -0,0 +1,147 @@
+#!/bin/bash -l
+
+usage() { echo "Usage: $0 [-d basedirectory ]" 1>&2; exit 1; }
+
+DIRECTORY="."
+
+while getopts "d:" opt; do
+  case $opt in
+    d )
+        DIRECTORY=$OPTARG
+        ;;
+    h )
+        usage
+        ;;
+   \? )
+        usage
+        ;;
+  esac
+done
+
+cd $DIRECTORY
+
+#=====================================================================================
+cat > mdp_parameters.mdp << EOF
+integrator               =  INTEGRATOR 
+dt                       = 0.001
+nsteps                   =  NSTEPS 
+nstcomm                  = 10
+
+nstlog                   =  NLOG 
+nstcalcenergy            = 10
+nstenergy                =  NENERGY 
+nstxout-compressed       =  NSTXOUT 
+compressed-x-precision   = 1000
+energygrps               = system
+
+rlist                    = 1.2
+nstlist                  = 10
+
+coulombtype              = pme
+rcoulomb                 = 1.2
+coulomb-modifier         = potential-shift-verlet
+vdwtype                  = pme
+rvdw                     = 1.2
+vdw-modifier             = potential-shift-verlet
+fourierspacing           = 0.144
+
+tcoupl                   = v-rescale
+tau_t                    =  TAUT 
+gen_vel                  = yes
+gen_temp                 =  TEMP 
+ref_t                    =  TEMP 
+tc-grps                  = system
+
+pcoupl                   =  PCOUPL 
+tau_p                    =  TAUP 
+ref_p                    =  PRESSURE 
+compressibility          = 4.5e-5
+
+nstpcouple               = 10
+nsttcouple               = 10
+
+EOF
+
+#=====================================================================================
+cat > params_emin.ini << EOF
+INTEGRATOR = steep
+NSTEPS = 10000
+NLOG = 100
+NENERGY = 100
+NSTXOUT = 100
+TAUT = 1.0
+TEMP = 300
+PCOUPL = no
+TCOUPL = no
+TAUP = 1.0
+EOF
+
+cat > params_an1.ini << EOF
+INTEGRATOR = md
+NSTEPS = 2000000
+NLOG = 1000
+NENERGY = 100
+NSTXOUT = 1000
+TCOUPL = v-rescale
+TAUT = 0.5
+TEMP = 10.0
+PCOUPL = c-rescale
+TAUP = 1.0
+EOF
+
+#=====================================================================================
+
+cat > topology.top << EOF
+[ defaults ]
+; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
+  1             2               yes              1.0     1.0
+
+[atomtypes]
+;name     mass      charge   ptype    sigma        epsilon
+A     MASS       0.000       A      SIGMA_A         EPSILON_A 
+B     MASS       0.000       A      SIGMA_B         EPSILON_B 
+D     0             0.000       D   0.0           0.0
+
+[moleculetype]
+; name nrexcl
+L  1
+
+[atoms]
+; nr type resnr residu atom cgnr charge
+1     A   1     L  A    1     0        MASS 
+2     B   1     L  B1   1    CHARGE_B      MASS 
+3     B   1     L  B2   1    CHARGE_B      MASS 
+4     D   1     L  D    1    CHARGE_A      0.0
+
+[settles]
+;i      funct   doh     dhh
+1       1       D_AB     D_BB 
+
+
+[dummies3]
+; Dummy from                            funct       a        b
+4       1       2       3       1       DUMMY_AB      DUMMY_AB 
+
+[exclusions]
+1       2       3       4
+2       1       3       4
+3       1       2       4
+4       1       2       3
+
+[system]
+ MODEL 
+
+[molecules]
+L                 NMOL 
+EOF
+
+#=====================================================================================
+bash ../create_emin.sh
+bash ../create_annealing1.sh
+
+
+#=====================================================================================
+
+echo "finished and simulation directory $DIRECTORY created and filled"
+ls
+exit 0