Removed .html files. Removed compute.h mods. Cast pressure for functions (2e2f1977) · Commits · 郑智淋 / lammps

src/USER-BOCS/README

+0 −3

Original line number	Diff line number	Diff line
		@@ -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

src/USER-BOCS/bocs/methanol.lmp

+1 −5

Original line number	Diff line number	Diff line
		@@ -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

src/USER-BOCS/doc/fix_bocs.txt

+8 −20

Original line number	Diff line number	Diff line
		@@ -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:]

src/USER-BOCS/fix_bocs.cpp

+32 −26

Original line number	Diff line number	Diff line
		@@ -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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