small modification to fix bond/react to allow equal style variables as probability o (0288bb4b) · Commits · 郑智淋 / lammps

doc/src/fix_bond_react.rst

+4 −2

Original line number	Diff line number	Diff line
		@@ -419,8 +419,10 @@ it occurs:

		The prob keyword can affect whether or not an eligible reaction
		actually occurs. The fraction setting must be a value between 0.0 and
		1.0. A uniform random number between 0.0 and 1.0 is generated and the
		eligible reaction only occurs if the random number is less than the
		1.0 or can be an equal style variable. In the later case the variable
		is evaluated during runtime and adjusted to be between 0.0 and 1.0 if
		necessary. A uniform random number between 0.0 and 1.0 is generated and
		the eligible reaction only occurs if the random number is less than the
		fraction. Up to N reactions are permitted to occur, as optionally
		specified by the max_rxn keyword.

examples/USER/reaction/nylon,6-6_melt/in.large_nylon_melt_variable_probability

0 → 100644

+55 −0

Original line number	Diff line number	Diff line
		# 35,000 atom nylon melt example

		units real

		boundary p p p

		atom_style full

		kspace_style pppm 1.0e-4

		pair_style lj/class2/coul/long 8.5

		angle_style class2

		bond_style class2

		dihedral_style class2

		improper_style class2

		read_data large_nylon_melt.data.gz

		variable runsteps equal 200
		varaible prob equal step/v_runsteps

		velocity all create 800.0 4928459 dist gaussian

		molecule mol1 rxn1_stp1_unreacted.data_template
		molecule mol2 rxn1_stp1_reacted.data_template
		molecule mol3 rxn1_stp2_unreacted.data_template
		molecule mol4 rxn1_stp2_reacted.data_template

		thermo 50

		# dump 1 all xyz 100 test_vis.xyz

		fix myrxns all bond/react stabilization yes statted_grp .03 &
		react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map &
		react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map

		# stable at 800K
		fix 1 statted_grp_REACT nvt temp 800 800 100

		# in order to customize behavior of reacting atoms,
		# you can use the internally created 'bond_react_MASTER_group', like so:
		# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1

		thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts

		# restart 100 restart1 restart2

		run 200

		# write_restart restart_longrun
		# write_data restart_longrun.data

src/USER-REACTION/fix_bond_react.cpp

+33 −2

Original line number	Diff line number	Diff line
		@@ -39,6 +39,8 @@ Contributing Author: Jacob Gissinger (jacob.gissinger@colorado.edu)
		#include "math_extra.h"
		#include "memory.h"
		#include "error.h"
		#include "input.h"
		#include "variable.h"

		#include <algorithm>

		@@ -175,6 +177,8 @@ FixBondReact::FixBondReact(LAMMPS lmp, int narg, char *arg) :
		memory->create(nghostlyskips,nreacts,"bond/react:nghostlyskips");
		memory->create(seed,nreacts,"bond/react:seed");
		memory->create(limit_duration,nreacts,"bond/react:limit_duration");
		memory->create(var_fraction_flag,nreacts,"bond/react:var_fraction_flag");
		memory->create(var_fraction_id,nreacts,"bond/react:var_fraction_id");
		memory->create(stabilize_steps_flag,nreacts,"bond/react:stabilize_steps_flag");
		memory->create(update_edges_flag,nreacts,"bond/react:update_edges_flag");
		memory->create(constraints,1,MAXCONARGS,"bond/react:constraints");
		@@ -193,6 +197,8 @@ FixBondReact::FixBondReact(LAMMPS lmp, int narg, char *arg) :
		fraction[i] = 1;
		seed[i] = 12345;
		max_rxn[i] = INT_MAX;
		var_fraction_flag[i] = 0;
		var_fraction_id[i] = 0;
		stabilize_steps_flag[i] = 0;
		update_edges_flag[i] = 0;
		// set default limit duration to 60 timesteps
		@@ -251,7 +257,23 @@ FixBondReact::FixBondReact(LAMMPS lmp, int narg, char *arg) :
		if (strcmp(arg[iarg],"prob") == 0) {
		if (iarg+3 > narg) error->all(FLERR,"Illegal fix bond/react command: "
		"'prob' keyword has too few arguments");
		// check if probability is a variable
		if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) {
		int n = strlen(&arg[iarg+1][2]) + 1;
		char *fracstr = new char[n];
		strcpy(fracstr,&arg[iarg+1][2]);
		var_fraction_id[rxn] = input->variable->find(fracstr);
		if (var_fraction_id[rxn] < 0)
		error->all(FLERR,"variable name for fix bond/react does not exist");
		if (! input->variable->equalstyle(var_fraction_id[rxn]))
		error->all(FLERR,"variable in bond/react is not equal style");
		fraction[rxn] = input->variable->compute_equal(var_fraction_id[rxnID]);
		var_fraction_flag[rxn] = 1.0;
		delete [] fracstr;
		} else {
		// otherwise probability should be a number
		fraction[rxn] = force->numeric(FLERR,arg[iarg+1]);
		}
		seed[rxn] = force->inumeric(FLERR,arg[iarg+2]);
		if (fraction[rxn] < 0.0 \|\| fraction[rxn] > 1.0)
		error->all(FLERR,"Illegal fix bond/react command: "
		@@ -447,6 +469,8 @@ FixBondReact::~FixBondReact()
		memory->destroy(nlocalskips);
		memory->destroy(nghostlyskips);
		memory->destroy(limit_duration);
		memory->destroy(var_fraction_flag);
		memory->destroy(var_fraction_id);
		memory->destroy(stabilize_steps_flag);
		memory->destroy(update_edges_flag);

		@@ -824,6 +848,13 @@ void FixBondReact::post_integrate()
		comm->reverse_comm_fix(this);
		}

		// update reaction probability
		if (var_fraction_flag[rxnID]) {
		fraction[rxnID] = input->variable->compute_equal(var_fraction_id[rxnID]);
		if (fraction[rxnID] < 0.0) fraction[rxnID] = 0.0;
		if (fraction[rxnID] > 1.0) fraction[rxnID] = 1.0;
		}

		// each atom now knows its winning partner
		// for prob check, generate random value for each atom with a bond partner
		// forward comm of partner and random value, so ghosts have it

src/USER-REACTION/fix_bond_react.h

+1 −0

Original line number	Diff line number	Diff line
		@@ -64,6 +64,7 @@ class FixBondReact : public Fix {
		int custom_exclude_flag;
		int *stabilize_steps_flag;
		int *update_edges_flag;
		int var_fraction_flag, var_fraction_id;
		int nconstraints;
		int narrhenius;
		double **constraints;

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