#!/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