Hi Christoph, I think I have it basically working now, but I might be having a few issues. Here is what I did
1) I created a calc_pressure_lammps.sh file as you suggested. It is
attached, but it is basically just calculating the average of a column of
pressures I've outputted from LAMMPS using awk and assigning this to the
p_new variable. I have hard coded the name of the lammps file (called
lammps.pressure), as I wasn't sure how this could be read into the script.
2)
Added "pressure lammps calc_pressure_lammps.sh" in csg_table below
"pressure gromacs calc_pressure_gromacs.sh"
3) Commented out in postupd_pressure.sh this line
#[[ $sim_prog != gromacs ]] && die "${0##*/}: pressure correction for
${sim_prog} is not implemented yet!"
4) It seems to be running and the pressure appears to be improving. I have
3 bead types for the hexane example, and 3 interactions, A-A, B-B, and
A-B. VOTCA is only writing a A-A.pressure and a A-B.pressure file. It
doesn't seem to be writing a B-B.pressure file, so I'm not sure if it is
updating the B-B interaction??
I am attaching the settings.xml file where I am calling for the pressure
correction. Can you take a look to see if it is defined correctly there?
In the *tar.gz I am attaching my current version of the ibi for LAMMPS with
real units and pressure correction.
Thanks again for all your help.
Josh
On Wednesday, February 15, 2017 at 11:05:47 AM UTC-5, Joshua Moore wrote:
> Hello,
>
> It appears the pressure correction for LAMMPS is not implemented.
>
> I saw this post by Frank
>
> https://groups.google.com/d/msg/votca/Jxsdz6v9QKw/OUVfYan8CwAJ
>
> It seems like in order to make it work, you would just have to feed in the
> pressure from LAMMPS.
>
> What would be required for this?
>
> Could I have LAMMPS output an average pressure, and then this could be fed
> into pressure_cor_simple.pl as my $p_now=$ARGV[0]; ??
>
> How does Gromacs do it? Does Gromacs calculate an average pressure and
> that is fed in as $ARGV[0] into the perl script?
>
> Thanks.
>
> Josh
>
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toVotca.tar.gz
Description: Binary data
#! /bin/bash # # Copyright 2009-2015 The VOTCA Development Team (http://www.votca.org) # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. # if [[ $1 = "--help" ]]; then cat <<EOF ${0##*/}, version %version% This script calcs the pressure for lammps and writes it to outfile Usage: ${0##*/} outfile Used external packages: lammps EOF exit 0 fi [[ -z $1 ]] && die "${0##*/}: Missing argument" p_now=$(awk 'NR > 1 {avg += $1} END {printf "%.16f\n", avg/(NR-1)}' lammps.press) echo "Pressure=${p_now}" > "$1"
settings.xml
Description: XML document
