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Update wall density in mdp files
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@alec-glisman
alec-glisman committed Feb 27, 2024
1 parent 753ca89 commit db87017
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Showing 8 changed files with 17 additions and 17 deletions.
4 changes: 2 additions & 2 deletions parameters/mdp/energy-minimization/em.mdp
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Expand Up @@ -52,6 +52,6 @@ freezegrps = Crystal ; groups that are to be frozen
freezedim = Y Y Y ; directions in which the groups are frozen
;;; Vacuum parameters ;;;
nwall = 0 ; number of walls
wall-type = 9-3 ; type of wall potential
wall-type = 9-3 ; type of wall potential
wall-atomtype = WR WL ; the atom type name in the force field for each wall.
wall-density = 12 12 ; [nm-3] / [nm-2] the number density of the atoms for each wall
wall-density = 0.1 0.1 ; [nm-3] / [nm-2] the number density of the atoms for each wall
4 changes: 2 additions & 2 deletions parameters/mdp/molecular-dynamics/npt_eqbm.mdp
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Expand Up @@ -57,6 +57,6 @@ lincs-iter = 1 ; number of iterative corrections to ma
lincs-warnangle = 30 ; print warning to log file and stderr if bond rotations be more than this angle
;;; Vacuum parameters ;;;
nwall = 0 ; number of walls
wall-type = 9-3 ; type of wall potential
wall-type = 9-3 ; type of wall potential
wall-atomtype = WR WL ; the atom type name in the force field for each wall.
wall-density = 12 12 ; [nm-3] / [nm-2] the number density of the atoms for each wall
wall-density = 0.1 0.1 ; [nm-3] / [nm-2] the number density of the atoms for each wall
4 changes: 2 additions & 2 deletions parameters/mdp/molecular-dynamics/npt_prod_100ns.mdp
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Original file line number Diff line number Diff line change
Expand Up @@ -56,6 +56,6 @@ lincs-iter = 1 ; number of iterative corrections to ma
lincs-warnangle = 30 ; print warning to log file and stderr if bond rotations be more than this angle
;;; Vacuum parameters ;;;
nwall = 0 ; number of walls
wall-type = 9-3 ; type of wall potential
wall-type = 9-3 ; type of wall potential
wall-atomtype = WR WL ; the atom type name in the force field for each wall.
wall-density = 12 12 ; [nm-3] / [nm-2] the number density of the atoms for each wall
wall-density = 0.1 0.1 ; [nm-3] / [nm-2] the number density of the atoms for each wall
4 changes: 2 additions & 2 deletions parameters/mdp/molecular-dynamics/npt_prod_500ns.mdp
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Original file line number Diff line number Diff line change
Expand Up @@ -56,6 +56,6 @@ lincs-iter = 1 ; number of iterative corrections to ma
lincs-warnangle = 30 ; print warning to log file and stderr if bond rotations be more than this angle
;;; Vacuum parameters ;;;
nwall = 0 ; number of walls
wall-type = 9-3 ; type of wall potential
wall-type = 9-3 ; type of wall potential
wall-atomtype = WR WL ; the atom type name in the force field for each wall.
wall-density = 12 12 ; [nm-3] / [nm-2] the number density of the atoms for each wall
wall-density = 0.1 0.1 ; [nm-3] / [nm-2] the number density of the atoms for each wall
4 changes: 2 additions & 2 deletions parameters/mdp/molecular-dynamics/nvt_eqbm.mdp
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Original file line number Diff line number Diff line change
Expand Up @@ -55,6 +55,6 @@ freezegrps = Frozen ; groups that are to be frozen
freezedim = Y Y Y ; directions in which the groups are frozen
;;; Vacuum parameters ;;;
nwall = 0 ; number of walls
wall-type = 9-3 ; type of wall potential
wall-type = 9-3 ; type of wall potential
wall-atomtype = WR WL ; the atom type name in the force field for each wall.
wall-density = 12 12 ; [nm-3] / [nm-2] the number density of the atoms for each wall
wall-density = 0.1 0.1 ; [nm-3] / [nm-2] the number density of the atoms for each wall
4 changes: 2 additions & 2 deletions parameters/mdp/molecular-dynamics/nvt_prod_100ns.mdp
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Original file line number Diff line number Diff line change
Expand Up @@ -55,6 +55,6 @@ freezegrps = Frozen ; groups that are to be frozen
freezedim = Y Y Y ; directions in which the groups are frozen
;;; Vacuum parameters ;;;
nwall = 0 ; number of walls
wall-type = 9-3 ; type of wall potential
wall-type = 9-3 ; type of wall potential
wall-atomtype = WR WL ; the atom type name in the force field for each wall.
wall-density = 12 12 ; [nm-3] / [nm-2] the number density of the atoms for each wall
wall-density = 0.1 0.1 ; [nm-3] / [nm-2] the number density of the atoms for each wall
4 changes: 2 additions & 2 deletions parameters/mdp/molecular-dynamics/nvt_prod_500ns.mdp
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Original file line number Diff line number Diff line change
Expand Up @@ -55,6 +55,6 @@ freezegrps = Frozen ; groups that are to be frozen
freezedim = Y Y Y ; directions in which the groups are frozen
;;; Vacuum parameters ;;;
nwall = 0 ; number of walls
wall-type = 9-3 ; type of wall potential
wall-type = 9-3 ; type of wall potential
wall-atomtype = WR WL ; the atom type name in the force field for each wall.
wall-density = 12 12 ; [nm-3] / [nm-2] the number density of the atoms for each wall
wall-density = 0.1 0.1 ; [nm-3] / [nm-2] the number density of the atoms for each wall
6 changes: 3 additions & 3 deletions scripts/method/initialization.sh
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Expand Up @@ -109,9 +109,9 @@ echo "INFO: Copying input files to working directory"

# add vacuum parameters to mdp file
if [[ "${VACUUM_HEIGHT}" -gt 0 ]]; then
sed -i 's/^ewald-geometry .*/ewald-geometry = 3dc/g' "${sim_name}.mdp" || exit 1
sed -i 's/^pbc .*/pbc = xy/g' "${sim_name}.mdp" || exit 1
sed -i 's/^nwall .*/nwall = 2/g' "${sim_name}.mdp" || exit 1
sed -i 's/^ewald-geometry .*/ewald-geometry = 3dc/g' "mdin.mdp"
sed -i 's/^pbc .*/pbc = xy/g' "mdin.mdp"
sed -i 's/^nwall .*/nwall = 2/g' "mdin.mdp"
fi

} >>"${log_file}" 2>&1
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