git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3951 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
937
src/fix_npt.cpp
937
src/fix_npt.cpp
@ -11,193 +11,38 @@
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Mark Stevens (SNL)
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------------------------------------------------------------------------- */
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#include "string.h"
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#include "stdlib.h"
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#include "math.h"
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#include "fix_npt.h"
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#include "atom.h"
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#include "force.h"
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#include "comm.h"
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#include "modify.h"
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#include "fix_deform.h"
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#include "compute.h"
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#include "kspace.h"
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#include "update.h"
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#include "respa.h"
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#include "domain.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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#define MIN(A,B) ((A) < (B)) ? (A) : (B)
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#define MAX(A,B) ((A) > (B)) ? (A) : (B)
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enum{NOBIAS,BIAS};
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enum{XYZ,XY,YZ,XZ,ANISO};
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/* ---------------------------------------------------------------------- */
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FixNPT::FixNPT(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg)
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FixNH(lmp, narg, arg)
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{
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if (narg < 7) error->all("Illegal fix npt command");
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restart_global = 1;
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box_change = 1;
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time_integrate = 1;
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scalar_flag = 1;
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global_freq = 1;
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extscalar = 1;
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t_start = atof(arg[3]);
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t_stop = atof(arg[4]);
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double t_period = atof(arg[5]);
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if (t_start < 0.0 || t_stop <= 0.0)
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error->all("Target T for fix npt cannot be 0.0");
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double p_period[3];
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if (strcmp(arg[6],"xyz") == 0) {
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if (narg < 10) error->all("Illegal fix npt command");
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press_couple = XYZ;
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p_start[0] = p_start[1] = p_start[2] = atof(arg[7]);
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p_stop[0] = p_stop[1] = p_stop[2] = atof(arg[8]);
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p_period[0] = p_period[1] = p_period[2] = atof(arg[9]);
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p_flag[0] = p_flag[1] = p_flag[2] = 1;
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if (domain->dimension == 2) {
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p_start[2] = p_stop[2] = p_period[2] = 0.0;
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p_flag[2] = 0;
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}
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} else {
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if (strcmp(arg[6],"xy") == 0) press_couple = XY;
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else if (strcmp(arg[6],"yz") == 0) press_couple = YZ;
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else if (strcmp(arg[6],"xz") == 0) press_couple = XZ;
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else if (strcmp(arg[6],"aniso") == 0) press_couple = ANISO;
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else error->all("Illegal fix npt command");
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if (narg < 14) error->all("Illegal fix npt command");
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if (domain->dimension == 2 &&
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(press_couple == XY || press_couple == YZ || press_couple == XZ))
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error->all("Invalid fix npt command for a 2d simulation");
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if (strcmp(arg[7],"NULL") == 0) {
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p_start[0] = p_stop[0] = p_period[0] = 0.0;
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p_flag[0] = 0;
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} else {
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p_start[0] = atof(arg[7]);
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p_stop[0] = atof(arg[8]);
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p_flag[0] = 1;
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}
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if (strcmp(arg[9],"NULL") == 0) {
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p_start[1] = p_stop[1] = p_period[1] = 0.0;
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p_flag[1] = 0;
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} else {
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p_start[1] = atof(arg[9]);
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p_stop[1] = atof(arg[10]);
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p_flag[1] = 1;
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}
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if (strcmp(arg[11],"NULL") == 0) {
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p_start[2] = p_stop[2] = p_period[2] = 0.0;
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p_flag[2] = 0;
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} else {
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if (domain->dimension == 2)
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error->all("Invalid fix npt command for a 2d simulation");
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p_start[2] = atof(arg[11]);
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p_stop[2] = atof(arg[12]);
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p_flag[2] = 1;
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}
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double period = atof(arg[13]);
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if (p_flag[0]) p_period[0] = period;
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if (p_flag[1]) p_period[1] = period;
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if (p_flag[2]) p_period[2] = period;
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}
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// process extra keywords
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drag = 0.0;
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allremap = 1;
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int iarg;
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if (press_couple == XYZ) iarg = 10;
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else iarg = 14;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"drag") == 0) {
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if (iarg+2 > narg) error->all("Illegal fix npt command");
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drag = atof(arg[iarg+1]);
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iarg += 2;
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} else if (strcmp(arg[iarg],"dilate") == 0) {
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if (iarg+2 > narg) error->all("Illegal fix npt command");
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if (strcmp(arg[iarg+1],"all") == 0) allremap = 1;
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else if (strcmp(arg[iarg+1],"partial") == 0) allremap = 0;
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else error->all("Illegal fix npt command");
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iarg += 2;
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} else error->all("Illegal fix npt command");
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}
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// error checks
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if (press_couple == XY && (p_flag[0] == 0 || p_flag[1] == 0))
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error->all("Invalid fix npt command pressure settings");
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if (press_couple == YZ && (p_flag[1] == 0 || p_flag[2] == 0))
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error->all("Invalid fix npt command pressure settings");
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if (press_couple == XZ && (p_flag[0] == 0 || p_flag[2] == 0))
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error->all("Invalid fix npt command pressure settings");
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if (press_couple == XY &&
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(p_start[0] != p_start[1] || p_stop[0] != p_stop[1]))
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error->all("Invalid fix npt command pressure settings");
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if (press_couple == YZ &&
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(p_start[1] != p_start[2] || p_stop[1] != p_stop[2]))
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error->all("Invalid fix npt command pressure settings");
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if (press_couple == XZ &&
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(p_start[0] != p_start[2] || p_stop[0] != p_stop[2]))
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error->all("Invalid fix npt command pressure settings");
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if (p_flag[0] && domain->xperiodic == 0)
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error->all("Cannot use fix npt on a non-periodic dimension");
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if (p_flag[1] && domain->yperiodic == 0)
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error->all("Cannot use fix npt on a non-periodic dimension");
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if (p_flag[2] && domain->zperiodic == 0)
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error->all("Cannot use fix npt on a non-periodic dimension");
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// convert input periods to frequencies
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if (t_period <= 0.0 || (p_flag[0] && p_period[0] <= 0.0) ||
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(p_flag[1] && p_period[1] <= 0.0) || (p_flag[2] && p_period[2] <= 0.0))
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error->all("Fix npt periods must be > 0.0");
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t_freq = 1.0 / t_period;
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p_freq[0] = p_freq[1] = p_freq[2] = 0.0;
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if (p_flag[0]) p_freq[0] = 1.0 / p_period[0];
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if (p_flag[1]) p_freq[1] = 1.0 / p_period[1];
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if (p_flag[2]) p_freq[2] = 1.0 / p_period[2];
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if (!tstat_flag)
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error->all("Temperature control must be used with fix npt");
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if (!pstat_flag)
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error->all("Pressure control must be used with fix npt");
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// create a new compute temp style
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// id = fix-ID + temp
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// compute group = all since pressure is always global (group all)
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// and thus its KE/temperature contribution should use group all
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// and thus its KE/temperature contribution should use group all
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int n = strlen(id) + 6;
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id_temp = new char[n];
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strcpy(id_temp,id);
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strcat(id_temp,"_temp");
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char **newarg = new char*[3];
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newarg[0] = id_temp;
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newarg[1] = (char *) "all";
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if (strcmp(style,"npt") == 0) newarg[2] = (char *) "temp";
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else if (strcmp(style,"npt/asphere") == 0)
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newarg[2] = (char *) "temp/asphere";
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else if (strcmp(style,"npt/sphere") == 0)
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newarg[2] = (char *) "temp/sphere";
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newarg[2] = (char *) "temp";
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modify->add_compute(3,newarg);
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delete [] newarg;
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tflag = 1;
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@ -210,7 +55,7 @@ FixNPT::FixNPT(LAMMPS *lmp, int narg, char **arg) :
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id_press = new char[n];
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strcpy(id_press,id);
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strcat(id_press,"_press");
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newarg = new char*[4];
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newarg[0] = id_press;
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newarg[1] = (char *) "all";
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@ -219,766 +64,4 @@ FixNPT::FixNPT(LAMMPS *lmp, int narg, char **arg) :
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modify->add_compute(4,newarg);
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delete [] newarg;
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pflag = 1;
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// Nose/Hoover temp and pressure init
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eta = eta_dot = 0.0;
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omega[0] = omega[1] = omega[2] = 0.0;
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omega_dot[0] = omega_dot[1] = omega_dot[2] = 0.0;
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nrigid = 0;
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rfix = NULL;
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}
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/* ---------------------------------------------------------------------- */
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FixNPT::~FixNPT()
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{
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delete [] rfix;
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// delete temperature and pressure if fix created them
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if (tflag) modify->delete_compute(id_temp);
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if (pflag) modify->delete_compute(id_press);
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delete [] id_temp;
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delete [] id_press;
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}
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/* ---------------------------------------------------------------------- */
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int FixNPT::setmask()
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{
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int mask = 0;
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mask |= INITIAL_INTEGRATE;
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mask |= FINAL_INTEGRATE;
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mask |= THERMO_ENERGY;
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mask |= INITIAL_INTEGRATE_RESPA;
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mask |= FINAL_INTEGRATE_RESPA;
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return mask;
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}
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/* ---------------------------------------------------------------------- */
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void FixNPT::init()
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{
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if (domain->triclinic) error->all("Cannot use fix npt with triclinic box");
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for (int i = 0; i < modify->nfix; i++)
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if (strcmp(modify->fix[i]->style,"deform") == 0) {
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int *dimflag = ((FixDeform *) modify->fix[i])->dimflag;
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if ((p_flag[0] && dimflag[0]) || (p_flag[1] && dimflag[1]) ||
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(p_flag[2] && dimflag[2]))
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error->all("Cannot use fix npt and fix deform on same dimension");
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}
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// set temperature and pressure ptrs
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int icompute = modify->find_compute(id_temp);
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if (icompute < 0) error->all("Temperature ID for fix npt does not exist");
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temperature = modify->compute[icompute];
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if (temperature->tempbias) which = BIAS;
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else which = NOBIAS;
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icompute = modify->find_compute(id_press);
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if (icompute < 0) error->all("Pressure ID for fix npt does not exist");
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pressure = modify->compute[icompute];
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// set timesteps and frequencies
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dtv = update->dt;
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dtf = 0.5 * update->dt * force->ftm2v;
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dthalf = 0.5 * update->dt;
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double freq = MAX(p_freq[0],p_freq[1]);
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freq = MAX(freq,p_freq[2]);
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drag_factor = 1.0 - (update->dt * freq * drag);
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boltz = force->boltz;
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nktv2p = force->nktv2p;
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dimension = domain->dimension;
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if (dimension == 3) vol0 = domain->xprd * domain->yprd * domain->zprd;
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else vol0 = domain->xprd * domain->yprd;
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if (force->kspace) kspace_flag = 1;
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else kspace_flag = 0;
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if (strcmp(update->integrate_style,"respa") == 0) {
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nlevels_respa = ((Respa *) update->integrate)->nlevels;
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step_respa = ((Respa *) update->integrate)->step;
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}
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// detect if any rigid fixes exist so rigid bodies move when box is remapped
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// rfix[] = indices to each fix rigid
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delete [] rfix;
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nrigid = 0;
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rfix = NULL;
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for (int i = 0; i < modify->nfix; i++)
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if (modify->fix[i]->rigid_flag) nrigid++;
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if (nrigid) {
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rfix = new int[nrigid];
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nrigid = 0;
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for (int i = 0; i < modify->nfix; i++)
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if (modify->fix[i]->rigid_flag) rfix[nrigid++] = i;
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}
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}
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/* ----------------------------------------------------------------------
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compute T,P before integrator starts
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------------------------------------------------------------------------- */
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void FixNPT::setup(int vflag)
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{
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t_target = t_start; // used by compute_scalar()
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p_target[0] = p_start[0];
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p_target[1] = p_start[1];
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p_target[2] = p_start[2];
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t_current = temperature->compute_scalar();
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if (press_couple == XYZ) {
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double tmp = pressure->compute_scalar();
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} else {
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temperature->compute_vector();
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pressure->compute_vector();
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}
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couple();
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// trigger virial computation on next timestep
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pressure->addstep(update->ntimestep+1);
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}
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/* ----------------------------------------------------------------------
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1st half of Verlet update
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------------------------------------------------------------------------- */
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void FixNPT::initial_integrate(int vflag)
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{
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int i;
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double dtfm;
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double delta = update->ntimestep - update->beginstep;
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delta /= update->endstep - update->beginstep;
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// update eta_dot
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t_target = t_start + delta * (t_stop-t_start);
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f_eta = t_freq*t_freq * (t_current/t_target - 1.0);
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eta_dot += f_eta*dthalf;
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eta_dot *= drag_factor;
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eta += dtv*eta_dot;
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// update omega_dot
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// for non-varying dims, p_freq is 0.0, so omega_dot doesn't change
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double f_omega,volume;
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if (dimension == 3) volume = domain->xprd*domain->yprd*domain->zprd;
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else volume = domain->xprd*domain->yprd;
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double denskt = atom->natoms*boltz*t_target / volume * nktv2p;
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for (i = 0; i < 3; i++) {
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p_target[i] = p_start[i] + delta * (p_stop[i]-p_start[i]);
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f_omega = p_freq[i]*p_freq[i] * (p_current[i]-p_target[i])/denskt;
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omega_dot[i] += f_omega*dthalf;
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omega_dot[i] *= drag_factor;
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omega[i] += dtv*omega_dot[i];
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factor[i] = exp(-dthalf*(eta_dot+omega_dot[i]));
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dilation[i] = exp(dthalf*omega_dot[i]);
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}
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// update v and x of atoms in group
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// for BIAS:
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// calculate temperature since some computes require temp
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// computed on current nlocal atoms to remove bias
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// OK to not test returned v = 0, since factor is multiplied by v
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double **x = atom->x;
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double **v = atom->v;
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double **f = atom->f;
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double *rmass = atom->rmass;
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double *mass = atom->mass;
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int *type = atom->type;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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if (igroup == atom->firstgroup) nlocal = atom->nfirst;
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if (rmass) {
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if (which == NOBIAS) {
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for (i = 0; i < nlocal; i++) {
|
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if (mask[i] & groupbit) {
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dtfm = dtf / rmass[i];
|
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v[i][0] = v[i][0]*factor[0] + dtfm*f[i][0];
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v[i][1] = v[i][1]*factor[1] + dtfm*f[i][1];
|
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v[i][2] = v[i][2]*factor[2] + dtfm*f[i][2];
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}
|
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}
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} else {
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double tmp = temperature->compute_scalar();
|
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for (i = 0; i < nlocal; i++) {
|
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if (mask[i] & groupbit) {
|
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temperature->remove_bias(i,v[i]);
|
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dtfm = dtf / rmass[i];
|
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v[i][0] = v[i][0]*factor[0] + dtfm*f[i][0];
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v[i][1] = v[i][1]*factor[1] + dtfm*f[i][1];
|
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v[i][2] = v[i][2]*factor[2] + dtfm*f[i][2];
|
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temperature->restore_bias(i,v[i]);
|
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}
|
||||
}
|
||||
}
|
||||
|
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} else {
|
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if (which == NOBIAS) {
|
||||
for (i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
dtfm = dtf / mass[type[i]];
|
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v[i][0] = v[i][0]*factor[0] + dtfm*f[i][0];
|
||||
v[i][1] = v[i][1]*factor[1] + dtfm*f[i][1];
|
||||
v[i][2] = v[i][2]*factor[2] + dtfm*f[i][2];
|
||||
}
|
||||
}
|
||||
} else {
|
||||
double tmp = temperature->compute_scalar();
|
||||
for (i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
temperature->remove_bias(i,v[i]);
|
||||
dtfm = dtf / mass[type[i]];
|
||||
v[i][0] = v[i][0]*factor[0] + dtfm*f[i][0];
|
||||
v[i][1] = v[i][1]*factor[1] + dtfm*f[i][1];
|
||||
v[i][2] = v[i][2]*factor[2] + dtfm*f[i][2];
|
||||
temperature->restore_bias(i,v[i]);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// remap simulation box by 1/2 step
|
||||
|
||||
remap();
|
||||
|
||||
// update x by full step for atoms in group
|
||||
|
||||
for (i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
x[i][0] += dtv * v[i][0];
|
||||
x[i][1] += dtv * v[i][1];
|
||||
x[i][2] += dtv * v[i][2];
|
||||
}
|
||||
}
|
||||
|
||||
// remap simulation box by 1/2 step
|
||||
// redo KSpace coeffs since volume has changed
|
||||
|
||||
remap();
|
||||
if (kspace_flag) force->kspace->setup();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
2nd half of Verlet update
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixNPT::final_integrate()
|
||||
{
|
||||
int i;
|
||||
double dtfm;
|
||||
|
||||
// update v of atoms in group
|
||||
// for BIAS:
|
||||
// calculate temperature since some computes require temp
|
||||
// computed on current nlocal atoms to remove bias
|
||||
// OK to not test returned v = 0, since factor is multiplied by v
|
||||
|
||||
double **v = atom->v;
|
||||
double **f = atom->f;
|
||||
double *rmass = atom->rmass;
|
||||
double *mass = atom->mass;
|
||||
int *type = atom->type;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
|
||||
|
||||
if (rmass) {
|
||||
if (which == NOBIAS) {
|
||||
for (i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
dtfm = dtf / rmass[i];
|
||||
v[i][0] = (v[i][0] + dtfm*f[i][0]) * factor[0];
|
||||
v[i][1] = (v[i][1] + dtfm*f[i][1]) * factor[1];
|
||||
v[i][2] = (v[i][2] + dtfm*f[i][2]) * factor[2];
|
||||
}
|
||||
}
|
||||
} else {
|
||||
double tmp = temperature->compute_scalar();
|
||||
for (i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
temperature->remove_bias(i,v[i]);
|
||||
dtfm = dtf / rmass[i];
|
||||
v[i][0] = (v[i][0] + dtfm*f[i][0]) * factor[0];
|
||||
v[i][1] = (v[i][1] + dtfm*f[i][1]) * factor[1];
|
||||
v[i][2] = (v[i][2] + dtfm*f[i][2]) * factor[2];
|
||||
temperature->restore_bias(i,v[i]);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
} else {
|
||||
if (which == NOBIAS) {
|
||||
for (i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
dtfm = dtf / mass[type[i]];
|
||||
v[i][0] = (v[i][0] + dtfm*f[i][0]) * factor[0];
|
||||
v[i][1] = (v[i][1] + dtfm*f[i][1]) * factor[1];
|
||||
v[i][2] = (v[i][2] + dtfm*f[i][2]) * factor[2];
|
||||
}
|
||||
}
|
||||
} else {
|
||||
double tmp = temperature->compute_scalar();
|
||||
for (i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
temperature->remove_bias(i,v[i]);
|
||||
dtfm = dtf / mass[type[i]];
|
||||
v[i][0] = (v[i][0] + dtfm*f[i][0]) * factor[0];
|
||||
v[i][1] = (v[i][1] + dtfm*f[i][1]) * factor[1];
|
||||
v[i][2] = (v[i][2] + dtfm*f[i][2]) * factor[2];
|
||||
temperature->restore_bias(i,v[i]);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// compute new T,P
|
||||
|
||||
t_current = temperature->compute_scalar();
|
||||
if (press_couple == XYZ) {
|
||||
double tmp = pressure->compute_scalar();
|
||||
} else {
|
||||
temperature->compute_vector();
|
||||
pressure->compute_vector();
|
||||
}
|
||||
couple();
|
||||
|
||||
// trigger virial computation on next timestep
|
||||
|
||||
pressure->addstep(update->ntimestep+1);
|
||||
|
||||
// update eta_dot
|
||||
|
||||
f_eta = t_freq*t_freq * (t_current/t_target - 1.0);
|
||||
eta_dot += f_eta*dthalf;
|
||||
eta_dot *= drag_factor;
|
||||
|
||||
// update omega_dot
|
||||
// for non-varying dims, p_freq is 0.0, so omega_dot doesn't change
|
||||
|
||||
double f_omega,volume;
|
||||
if (dimension == 3) volume = domain->xprd*domain->yprd*domain->zprd;
|
||||
else volume = domain->xprd*domain->yprd;
|
||||
double denskt = atom->natoms*boltz*t_target / volume * nktv2p;
|
||||
|
||||
for (i = 0; i < 3; i++) {
|
||||
f_omega = p_freq[i]*p_freq[i] * (p_current[i]-p_target[i])/denskt;
|
||||
omega_dot[i] += f_omega*dthalf;
|
||||
omega_dot[i] *= drag_factor;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixNPT::initial_integrate_respa(int vflag, int ilevel, int iloop)
|
||||
{
|
||||
// set timesteps by level
|
||||
|
||||
double dtfm;
|
||||
dtv = step_respa[ilevel];
|
||||
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
|
||||
dthalf = 0.5 * step_respa[ilevel];
|
||||
|
||||
// atom quantities
|
||||
|
||||
double **x = atom->x;
|
||||
double **v = atom->v;
|
||||
double **f = atom->f;
|
||||
double *rmass = atom->rmass;
|
||||
double *mass = atom->mass;
|
||||
int *type = atom->type;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
|
||||
|
||||
// outermost level - update eta_dot and omega_dot, apply to v, remap box
|
||||
// all other levels - NVE update of v
|
||||
// x,v updates performed for atoms in group
|
||||
|
||||
if (ilevel == nlevels_respa-1) {
|
||||
|
||||
double delta = update->ntimestep - update->beginstep;
|
||||
delta /= update->endstep - update->beginstep;
|
||||
|
||||
// update eta_dot
|
||||
|
||||
t_target = t_start + delta * (t_stop-t_start);
|
||||
f_eta = t_freq*t_freq * (t_current/t_target - 1.0);
|
||||
eta_dot += f_eta*dthalf;
|
||||
eta_dot *= drag_factor;
|
||||
eta += dtv*eta_dot;
|
||||
|
||||
// update omega_dot
|
||||
// for non-varying dims, p_freq is 0.0, so omega_dot doesn't change
|
||||
|
||||
double f_omega,volume;
|
||||
if (dimension == 3) volume = domain->xprd*domain->yprd*domain->zprd;
|
||||
else volume = domain->xprd*domain->yprd;
|
||||
double denskt = atom->natoms*boltz*t_target / volume * nktv2p;
|
||||
|
||||
for (int i = 0; i < 3; i++) {
|
||||
p_target[i] = p_start[i] + delta * (p_stop[i]-p_start[i]);
|
||||
f_omega = p_freq[i]*p_freq[i] * (p_current[i]-p_target[i])/denskt;
|
||||
omega_dot[i] += f_omega*dthalf;
|
||||
omega_dot[i] *= drag_factor;
|
||||
omega[i] += dtv*omega_dot[i];
|
||||
factor[i] = exp(-dthalf*(eta_dot+omega_dot[i]));
|
||||
dilation[i] = exp(dthalf*omega_dot[i]);
|
||||
}
|
||||
|
||||
// update v for atoms in group
|
||||
|
||||
if (rmass) {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
dtfm = dtf / rmass[i];
|
||||
v[i][0] = v[i][0]*factor[0] + dtfm*f[i][0];
|
||||
v[i][1] = v[i][1]*factor[1] + dtfm*f[i][1];
|
||||
v[i][2] = v[i][2]*factor[2] + dtfm*f[i][2];
|
||||
}
|
||||
}
|
||||
} else {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
dtfm = dtf / mass[type[i]];
|
||||
v[i][0] = v[i][0]*factor[0] + dtfm*f[i][0];
|
||||
v[i][1] = v[i][1]*factor[1] + dtfm*f[i][1];
|
||||
v[i][2] = v[i][2]*factor[2] + dtfm*f[i][2];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// remap simulation box by 1/2 step
|
||||
|
||||
remap();
|
||||
remap2flag = 1;
|
||||
|
||||
} else {
|
||||
|
||||
// update v for atoms in group
|
||||
|
||||
if (rmass) {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
dtfm = dtf / rmass[i];
|
||||
v[i][0] += dtfm*f[i][0];
|
||||
v[i][1] += dtfm*f[i][1];
|
||||
v[i][2] += dtfm*f[i][2];
|
||||
}
|
||||
}
|
||||
|
||||
} else {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
dtfm = dtf / mass[type[i]];
|
||||
v[i][0] += dtfm*f[i][0];
|
||||
v[i][1] += dtfm*f[i][1];
|
||||
v[i][2] += dtfm*f[i][2];
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// innermost level - also update x for atoms in group
|
||||
// if remap2flag:
|
||||
// this is 1st call at innermost level from rRESPA after 1st half remap
|
||||
// perform 2nd half of box remap
|
||||
// redo KSpace coeffs since volume has changed
|
||||
|
||||
if (ilevel == 0) {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
x[i][0] += dtv * v[i][0];
|
||||
x[i][1] += dtv * v[i][1];
|
||||
x[i][2] += dtv * v[i][2];
|
||||
}
|
||||
}
|
||||
if (remap2flag) {
|
||||
remap();
|
||||
if (kspace_flag) force->kspace->setup();
|
||||
remap2flag = 0;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixNPT::final_integrate_respa(int ilevel, int iloop)
|
||||
{
|
||||
double dtfm;
|
||||
|
||||
// set timesteps by level
|
||||
|
||||
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
|
||||
dthalf = 0.5 * step_respa[ilevel];
|
||||
|
||||
// outermost level - update eta_dot and omega_dot,
|
||||
// apply to v via final_integrate()
|
||||
// all other levels - NVE update of v
|
||||
// update v for atoms in group
|
||||
|
||||
if (ilevel == nlevels_respa-1) final_integrate();
|
||||
else {
|
||||
|
||||
// update v for atoms in group
|
||||
|
||||
double **v = atom->v;
|
||||
double **f = atom->f;
|
||||
double *rmass = atom->rmass;
|
||||
double *mass = atom->mass;
|
||||
int *type = atom->type;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
|
||||
|
||||
if (rmass) {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
dtfm = dtf / rmass[i];
|
||||
v[i][0] += dtfm*f[i][0];
|
||||
v[i][1] += dtfm*f[i][1];
|
||||
v[i][2] += dtfm*f[i][2];
|
||||
}
|
||||
}
|
||||
|
||||
} else {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
dtfm = dtf / mass[type[i]];
|
||||
v[i][0] += dtfm*f[i][0];
|
||||
v[i][1] += dtfm*f[i][1];
|
||||
v[i][2] += dtfm*f[i][2];
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixNPT::couple()
|
||||
{
|
||||
double *tensor = pressure->vector;
|
||||
|
||||
if (press_couple == XYZ)
|
||||
p_current[0] = p_current[1] = p_current[2] = pressure->scalar;
|
||||
else if (press_couple == XY) {
|
||||
double ave = 0.5 * (tensor[0] + tensor[1]);
|
||||
p_current[0] = p_current[1] = ave;
|
||||
p_current[2] = tensor[2];
|
||||
} else if (press_couple == YZ) {
|
||||
double ave = 0.5 * (tensor[1] + tensor[2]);
|
||||
p_current[1] = p_current[2] = ave;
|
||||
p_current[0] = tensor[0];
|
||||
} else if (press_couple == XZ) {
|
||||
double ave = 0.5 * (tensor[0] + tensor[2]);
|
||||
p_current[0] = p_current[2] = ave;
|
||||
p_current[1] = tensor[1];
|
||||
} else if (press_couple == ANISO) {
|
||||
p_current[0] = tensor[0];
|
||||
p_current[1] = tensor[1];
|
||||
p_current[2] = tensor[2];
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
change box size
|
||||
remap all atoms or fix group atoms depending on allremap flag
|
||||
if rigid bodies exist, scale rigid body centers-of-mass
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixNPT::remap()
|
||||
{
|
||||
int i;
|
||||
double oldlo,oldhi,ctr;
|
||||
|
||||
double **x = atom->x;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
// convert pertinent atoms and rigid bodies to lamda coords
|
||||
|
||||
if (allremap) domain->x2lamda(nlocal);
|
||||
else {
|
||||
for (i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit)
|
||||
domain->x2lamda(x[i],x[i]);
|
||||
}
|
||||
|
||||
if (nrigid)
|
||||
for (i = 0; i < nrigid; i++)
|
||||
modify->fix[rfix[i]]->deform(0);
|
||||
|
||||
// reset global and local box to new size/shape
|
||||
|
||||
for (i = 0; i < 3; i++) {
|
||||
if (p_flag[i]) {
|
||||
oldlo = domain->boxlo[i];
|
||||
oldhi = domain->boxhi[i];
|
||||
ctr = 0.5 * (oldlo + oldhi);
|
||||
domain->boxlo[i] = (oldlo-ctr)*dilation[i] + ctr;
|
||||
domain->boxhi[i] = (oldhi-ctr)*dilation[i] + ctr;
|
||||
}
|
||||
}
|
||||
|
||||
domain->set_global_box();
|
||||
domain->set_local_box();
|
||||
|
||||
// convert pertinent atoms and rigid bodies back to box coords
|
||||
|
||||
if (allremap) domain->lamda2x(nlocal);
|
||||
else {
|
||||
for (i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit)
|
||||
domain->lamda2x(x[i],x[i]);
|
||||
}
|
||||
|
||||
if (nrigid)
|
||||
for (i = 0; i < nrigid; i++)
|
||||
modify->fix[rfix[i]]->deform(1);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
pack entire state of Fix into one write
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixNPT::write_restart(FILE *fp)
|
||||
{
|
||||
int n = 0;
|
||||
double list[8];
|
||||
list[n++] = eta;
|
||||
list[n++] = eta_dot;
|
||||
list[n++] = omega[0];
|
||||
list[n++] = omega[1];
|
||||
list[n++] = omega[2];
|
||||
list[n++] = omega_dot[0];
|
||||
list[n++] = omega_dot[1];
|
||||
list[n++] = omega_dot[2];
|
||||
|
||||
if (comm->me == 0) {
|
||||
int size = n * sizeof(double);
|
||||
fwrite(&size,sizeof(int),1,fp);
|
||||
fwrite(list,sizeof(double),n,fp);
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
use state info from restart file to restart the Fix
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixNPT::restart(char *buf)
|
||||
{
|
||||
int n = 0;
|
||||
double *list = (double *) buf;
|
||||
eta = list[n++];
|
||||
eta_dot = list[n++];
|
||||
omega[0] = list[n++];
|
||||
omega[1] = list[n++];
|
||||
omega[2] = list[n++];
|
||||
omega_dot[0] = list[n++];
|
||||
omega_dot[1] = list[n++];
|
||||
omega_dot[2] = list[n++];
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int FixNPT::modify_param(int narg, char **arg)
|
||||
{
|
||||
if (strcmp(arg[0],"temp") == 0) {
|
||||
if (narg < 2) error->all("Illegal fix_modify command");
|
||||
if (tflag) {
|
||||
modify->delete_compute(id_temp);
|
||||
tflag = 0;
|
||||
}
|
||||
delete [] id_temp;
|
||||
int n = strlen(arg[1]) + 1;
|
||||
id_temp = new char[n];
|
||||
strcpy(id_temp,arg[1]);
|
||||
|
||||
int icompute = modify->find_compute(arg[1]);
|
||||
if (icompute < 0) error->all("Could not find fix_modify temperature ID");
|
||||
temperature = modify->compute[icompute];
|
||||
|
||||
if (temperature->tempflag == 0)
|
||||
error->all("Fix_modify temperature ID does not compute temperature");
|
||||
if (temperature->igroup != 0 && comm->me == 0)
|
||||
error->warning("Temperature for fix modify is not for group all");
|
||||
|
||||
// reset id_temp of pressure to new temperature ID
|
||||
|
||||
icompute = modify->find_compute(id_press);
|
||||
if (icompute < 0) error->all("Pressure ID for fix modify does not exist");
|
||||
modify->compute[icompute]->reset_extra_compute_fix(id_temp);
|
||||
|
||||
return 2;
|
||||
|
||||
} else if (strcmp(arg[0],"press") == 0) {
|
||||
if (narg < 2) error->all("Illegal fix_modify command");
|
||||
if (pflag) {
|
||||
modify->delete_compute(id_press);
|
||||
pflag = 0;
|
||||
}
|
||||
delete [] id_press;
|
||||
int n = strlen(arg[1]) + 1;
|
||||
id_press = new char[n];
|
||||
strcpy(id_press,arg[1]);
|
||||
|
||||
int icompute = modify->find_compute(arg[1]);
|
||||
if (icompute < 0) error->all("Could not find fix_modify pressure ID");
|
||||
pressure = modify->compute[icompute];
|
||||
|
||||
if (pressure->pressflag == 0)
|
||||
error->all("Fix_modify pressure ID does not compute pressure");
|
||||
return 2;
|
||||
}
|
||||
return 0;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double FixNPT::compute_scalar()
|
||||
{
|
||||
double ke = temperature->dof * boltz * t_target;
|
||||
double keplus = atom->natoms * boltz * t_target;
|
||||
double volume;
|
||||
if (dimension == 3) volume = domain->xprd * domain->yprd * domain->zprd;
|
||||
else volume = domain->xprd * domain->yprd;
|
||||
|
||||
int pdim = p_flag[0] + p_flag[1] + p_flag[2];
|
||||
|
||||
double energy = ke * (eta + 0.5*eta_dot*eta_dot/(t_freq*t_freq));
|
||||
for (int i = 0; i < 3; i++)
|
||||
if (p_freq[i] > 0.0)
|
||||
energy += 0.5*keplus*omega_dot[i]*omega_dot[i] /
|
||||
(p_freq[i]*p_freq[i]) + p_target[i]*(volume-vol0) / (pdim*nktv2p);
|
||||
|
||||
return energy;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixNPT::reset_dt()
|
||||
{
|
||||
dtv = update->dt;
|
||||
dtf = 0.5 * update->dt * force->ftm2v;
|
||||
dthalf = 0.5 * update->dt;
|
||||
|
||||
double freq = MAX(p_freq[0],p_freq[1]);
|
||||
freq = MAX(freq,p_freq[2]);
|
||||
drag_factor = 1.0 - (update->dt * freq * drag);
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user