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Removed .html files. Removed compute.h mods. Cast pressure for functions

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This commit is contained in:
MICHAEL ROBERT DELYSER
2018-05-02 11:14:30 -04:00
parent 56d0014a4a
commit 2e2f19770c
4 changed files with 42 additions and 55 deletions
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3
src/USER-BOCS/README
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@ -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

6
src/USER-BOCS/bocs/methanol.lmp
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@ -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

28
src/USER-BOCS/doc/fix_bocs.txt
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@ -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:]

60
src/USER-BOCS/fix_bocs.cpp
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@ -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~*/
}
@ -787,26 +785,6 @@ void FixBocs::init()
error->all(FLERR,"Cannot use fix npt and fix deform on "
"same component of stress tensor");
}
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);
}
else if ( p_basis_type == 1 || p_basis_type == 2 )
{
pressure->send_cg_info(p_basis_type, splines, spline_length);
}
}
else
{
error->all(FLERR,"Unable to find pressure. Are you sure you included"
" the compute bocsPress and fix_modify commands?");
}
}
}
// set temperature and pressure ptrs
@ -825,6 +803,33 @@ void FixBocs::init()
pressure = modify->compute[icompute];
}
if (pstat_flag)
{
if (p_match_flag) // MRD NJD
{
if (pressure)
{
if (p_basis_type == 0)
{
((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 )
{
((ComputePressureBocs *)pressure)->send_cg_info(p_basis_type,
splines, spline_length);
}
}
else
{
error->all(FLERR,"Unable to find pressure. Are you sure you included"
" the compute bocsPress and fix_modify commands?");
}
}
}
// set timesteps and frequencies
dtv = update->dt;
@ -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 );
}
}