From 2e2f19770c52cd25805a57a1698573fe69569ecf Mon Sep 17 00:00:00 2001
From: MICHAEL ROBERT DELYSER
<mrd5285@aci-lgn-004.acib.production.int.aci.ics.psu.edu>
Date: Wed, 2 May 2018 11:14:30 -0400
Subject: [PATCH] Removed .html files. Removed compute.h mods. Cast pressure
for functions
---
src/USER-BOCS/README | 3 --
src/USER-BOCS/bocs/methanol.lmp | 6 +---
src/USER-BOCS/doc/fix_bocs.txt | 28 +++++-----------
src/USER-BOCS/fix_bocs.cpp | 58 ++++++++++++++++++---------------
4 files changed, 41 insertions(+), 54 deletions(-)
diff --git a/src/USER-BOCS/README b/src/USER-BOCS/README
index 996375ccf7..001cb94d55 100644
--- a/src/USER-BOCS/README
+++ b/src/USER-BOCS/README
@@ -16,9 +16,6 @@ Dunn, NJH; Lebold, KM; DeLyser, MR; Rudzinski, JF; Noid, WG.
"BOCS: Bottom-Up Open-Source Coarse-Graining Software."
J. Phys. Chem. B. 122, 13, 3363-3377 (2018).
-The MOD_COMPUTE_H file is identical to the original compute.h except for
-the two lines (three with comments) needed for USER-BOCS to work.
-
Along with the source code files, the following files have been included
(in the /bocs/ directory):
methanol.lmp
diff --git a/src/USER-BOCS/bocs/methanol.lmp b/src/USER-BOCS/bocs/methanol.lmp
index 13a71aa67e..cb0a9420f0 100644
--- a/src/USER-BOCS/bocs/methanol.lmp
+++ b/src/USER-BOCS/bocs/methanol.lmp
@@ -42,12 +42,8 @@ variable UVDW equal evdwl*4.184
# ID group-ID style_name thermostat T_init T_end T_couple barostat P_start P_end P_couple pmatch_basis avg_vol N_sites N_coeffs coeff1 coeff2
fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 analytic 66476.015 968 2 245030.10 8962.20
-# Compute the modified pressure
-compute bocsPress all pressureBocs thermo_temp
# Report the modified pressure
-thermo_modify press bocsPress
-# Use the modified pressure for fix bocs instead of thermo_press
-fix_modify 1 press bocsPress
+thermo_modify press 1_press
diff --git a/src/USER-BOCS/doc/fix_bocs.txt b/src/USER-BOCS/doc/fix_bocs.txt
index e6b9013921..8824893d65 100644
--- a/src/USER-BOCS/doc/fix_bocs.txt
+++ b/src/USER-BOCS/doc/fix_bocs.txt
@@ -27,9 +27,7 @@ fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 analytic 66476.01
fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 cubic_spline input_Fv.dat :pre
-compute bocsPress all pressureBocs thermo_temp
-thermo_modify press bocsPress
-fix_modify 1 press bocsPress :pre
+thermo_modify press 1_press :pre
[Description:]
@@ -78,23 +76,13 @@ As this is computing a (modified) pressure, group-ID should be {all}.
The pressure correction has only been tested for use with an isotropic
pressure coupling in 3 dimensions.
-There are three additional commands that must be supplied along with fix
-bocs. They are given in the examples section. The name {bocsPress} can be
-changed for any name of your choosing, provided it remains consistent across
-all three commands. Additionally, the ID {1} in the {fix_modify} command must
-match up with the {ID} specified in the original {fix bocs} command. Everything else
-in those three commands must be unchanged. The first two commands can be
-specified before the {fix bocs} command, but the {fix_modify} command must be
-given after the original {fix bocs} command.
-
-The {compute} command tells LAMMPS to compute the pressure using the modified
-barostat.
-
-The {thermo_modify} command tells LAMMPS to report the pressure from the modified
-barostat instead of the default pressure, i.e. thermo_press.
-
-The {fix_modify} command tells LAMMPS to use the pressure from the modified
-barostat for the fix, instead of using the default presure, i.e. thermo_press.
+By default, LAMMPS will still report the normal value for the pressure
+if the pressure is printed via a {thermo} command, or if the pressures
+are written to a file every so often. In order to have LAMMPS report the
+modified pressure, you must include the {thermo_modify} command given in
+the examples. For the last argument in the command, you should put
+XXXX_press, where XXXX is the ID given to the fix bocs command (in the
+example, the ID of the fix bocs command is 1 ).
[Related:]
diff --git a/src/USER-BOCS/fix_bocs.cpp b/src/USER-BOCS/fix_bocs.cpp
index 3cc02d1ea4..94f28645d5 100644
--- a/src/USER-BOCS/fix_bocs.cpp
+++ b/src/USER-BOCS/fix_bocs.cpp
@@ -36,6 +36,8 @@
#include "error.h"
#include "citeme.h"
+#include "compute_pressure_bocs.h"
+
using namespace LAMMPS_NS;
using namespace FixConst;
@@ -225,9 +227,6 @@ FixBocs::FixBocs(LAMMPS *lmp, int narg, char **arg) :
"Supply a file name after cubic_spline.");
p_basis_type = 2;
spline_length = read_F_table( arg[iarg+1], p_basis_type );
-// build_cubic_splines(); MRD I moved this into read_F_table
-// and that's why I pass p_basis_type in there too. I was having
-// a fight getting "double ** data" stuff to work
iarg += 2;
} else
{
@@ -708,7 +707,6 @@ FixBocs::FixBocs(LAMMPS *lmp, int narg, char **arg) :
delete [] newarg;
pcomputeflag = 1;
-
/*~ MRD End of stuff copied from fix_npt.cpp~*/
}
@@ -787,18 +785,40 @@ void FixBocs::init()
error->all(FLERR,"Cannot use fix npt and fix deform on "
"same component of stress tensor");
}
+ }
+
+ // set temperature and pressure ptrs
+ int icompute = modify->find_compute(id_temp);
+ if (icompute < 0)
+ error->all(FLERR,"Temperature ID for fix bocs does not exist");
+ temperature = modify->compute[icompute];
+
+ if (temperature->tempbias) which = BIAS;
+ else which = NOBIAS;
+
+ if (pstat_flag) {
+ icompute = modify->find_compute(id_press);
+ if (icompute < 0)
+ error->all(FLERR,"Pressure ID for fix bocs does not exist");
+ pressure = modify->compute[icompute];
+ }
+
+
+ if (pstat_flag)
+ {
if (p_match_flag) // MRD NJD
- {
+ {
if (pressure)
{
if (p_basis_type == 0)
{
- pressure->send_cg_info(p_basis_type, N_p_match, p_match_coeffs,
- N_mol, vavg);
+ ((ComputePressureBocs *)pressure)->send_cg_info(p_basis_type,
+ N_p_match, p_match_coeffs, N_mol, vavg);
}
else if ( p_basis_type == 1 || p_basis_type == 2 )
{
- pressure->send_cg_info(p_basis_type, splines, spline_length);
+ ((ComputePressureBocs *)pressure)->send_cg_info(p_basis_type,
+ splines, spline_length);
}
}
else
@@ -809,21 +829,6 @@ void FixBocs::init()
}
}
- // set temperature and pressure ptrs
- int icompute = modify->find_compute(id_temp);
- if (icompute < 0)
- error->all(FLERR,"Temperature ID for fix bocs does not exist");
- temperature = modify->compute[icompute];
-
- if (temperature->tempbias) which = BIAS;
- else which = NOBIAS;
-
- if (pstat_flag) {
- icompute = modify->find_compute(id_press);
- if (icompute < 0)
- error->all(FLERR,"Pressure ID for fix bocs does not exist");
- pressure = modify->compute[icompute];
- }
// set timesteps and frequencies
@@ -1755,12 +1760,13 @@ int FixBocs::modify_param(int narg, char **arg)
{
if ( p_basis_type == 0 )
{
- pressure->send_cg_info(p_basis_type, N_p_match, p_match_coeffs,
- N_mol, vavg);
+ ((ComputePressureBocs *)pressure)->send_cg_info(p_basis_type, N_p_match,
+ p_match_coeffs, N_mol, vavg);
}
else if ( p_basis_type == 1 || p_basis_type == 2 )
{
- pressure->send_cg_info(p_basis_type, splines, spline_length );
+ ((ComputePressureBocs *)pressure)->send_cg_info(p_basis_type, splines,
+ spline_length );
}
}
--
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