git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@254 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
213
src/fix_npt.cpp
213
src/fix_npt.cpp
@ -1,7 +1,7 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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www.cs.sandia.gov/~sjplimp/lammps.html
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Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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@ -24,20 +24,22 @@
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#include "comm.h"
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#include "output.h"
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#include "modify.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 "temperature.h"
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#include "pressure.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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/* ---------------------------------------------------------------------- */
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FixNPT::FixNPT(int narg, char **arg) : Fix(narg, arg)
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FixNPT::FixNPT(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg)
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{
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if (narg < 7) error->all("Illegal fix npt command");
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@ -132,21 +134,6 @@ FixNPT::FixNPT(int narg, char **arg) : Fix(narg, arg)
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if (p_flag[2] && domain->zperiodic == 0)
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error->all("Cannot fix npt on a non-periodic dimension");
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// create a new temperature full style with fix ID and group all
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// pressure is always global (group all) and thus its
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// KE/temperature contribution should use group all
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eta = eta_dot = 0.0;
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char **newarg = new char*[3];
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newarg[0] = id;
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newarg[1] = "all";
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newarg[2] = "full";
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force->add_temp(3,newarg,1);
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delete [] newarg;
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temperature = force->find_temp(id);
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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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@ -159,9 +146,45 @@ FixNPT::FixNPT(int narg, char **arg) : Fix(narg, arg)
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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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// pressure init
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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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pressure = force->pressure;
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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] = "all";
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newarg[2] = "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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// create a new compute pressure style
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// id = fix-ID + press, compute group = all
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// pass id_temp as 4th arg to pressure constructor
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n = strlen(id) + 7;
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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] = "all";
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newarg[2] = "pressure";
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newarg[3] = id_temp;
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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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@ -174,6 +197,13 @@ FixNPT::FixNPT(int narg, char **arg) : Fix(narg, arg)
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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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@ -183,7 +213,7 @@ int FixNPT::setmask()
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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;
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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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@ -193,8 +223,27 @@ int FixNPT::setmask()
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void FixNPT::init()
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{
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if (atom->mass_require == 0)
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error->all("Cannot use fix npt with no per-type mass defined");
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if (atom->mass == NULL)
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error->all("Cannot use fix npt without per-type mass defined");
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// set temperature and pressure ptrs
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// set ptemperature only if pressure's id_pre is not id_temp
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int icompute = modify->find_compute(id_temp);
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if (icompute < 0) error->all("Temp ID for fix npt does not exist");
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temperature = modify->compute[icompute];
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icompute = modify->find_compute(id_press);
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if (icompute < 0) error->all("Press ID for fix npt does not exist");
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pressure = modify->compute[icompute];
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if (strcmp(id_temp,pressure->id_pre) == 0) ptemperature = NULL;
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else {
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icompute = modify->find_compute(pressure->id_pre);
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if (icompute < 0)
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error->all("Temp ID of press ID for fix npt does not exist");
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ptemperature = modify->compute[icompute];
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}
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// set timesteps and frequencies
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@ -247,13 +296,20 @@ void FixNPT::init()
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void FixNPT::setup()
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{
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t_target = t_start; // used by thermo_compute()
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t_target = t_start; // used by thermo()
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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();
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pressure->compute(temperature);
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t_current = temperature->compute_scalar();
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if (press_couple == 0) {
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if (ptemperature) double ptmp = ptemperature->compute_scalar();
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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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if (ptemperature) ptemperature->compute_vector();
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pressure->compute_vector();
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}
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couple();
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}
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@ -363,8 +419,15 @@ void FixNPT::final_integrate()
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// compute new T,P
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t_current = temperature->compute();
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pressure->compute(temperature);
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t_current = temperature->compute_scalar();
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if (press_couple == 0) {
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if (ptemperature) double ptmp = ptemperature->compute_scalar();
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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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if (ptemperature) ptemperature->compute_vector();
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pressure->compute_vector();
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}
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couple();
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// update eta_dot
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@ -537,26 +600,26 @@ void FixNPT::final_integrate_respa(int ilevel)
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void FixNPT::couple()
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{
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double *p_tensor = pressure->p_tensor;
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double *tensor = pressure->vector;
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if (press_couple == 0)
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p_current[0] = p_current[1] = p_current[2] = pressure->p_total;
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p_current[0] = p_current[1] = p_current[2] = pressure->scalar;
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else if (press_couple == 1) {
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double ave = 0.5 * (p_tensor[0] + p_tensor[1]);
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double ave = 0.5 * (tensor[0] + tensor[1]);
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p_current[0] = p_current[1] = ave;
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p_current[2] = p_tensor[2];
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p_current[2] = tensor[2];
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} else if (press_couple == 2) {
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double ave = 0.5 * (p_tensor[1] + p_tensor[2]);
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double ave = 0.5 * (tensor[1] + tensor[2]);
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p_current[1] = p_current[2] = ave;
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p_current[0] = p_tensor[0];
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p_current[0] = tensor[0];
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} else if (press_couple == 3) {
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double ave = 0.5 * (p_tensor[0] + p_tensor[2]);
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double ave = 0.5 * (tensor[0] + tensor[2]);
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p_current[0] = p_current[2] = ave;
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p_current[1] = p_tensor[1];
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p_current[1] = tensor[1];
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} if (press_couple == 4) {
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p_current[0] = p_tensor[0];
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p_current[1] = p_tensor[1];
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p_current[2] = p_tensor[2];
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p_current[0] = tensor[0];
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p_current[1] = tensor[1];
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p_current[2] = tensor[2];
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}
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}
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@ -694,13 +757,51 @@ int FixNPT::modify_param(int narg, char **arg)
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{
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if (strcmp(arg[0],"temp") == 0) {
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if (narg < 2) error->all("Illegal fix_modify command");
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temperature = force->find_temp(arg[1]);
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if (temperature == NULL)
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error->all("Could not find fix_modify temperature ID");
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if (tflag) {
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modify->delete_compute(id_temp);
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tflag = 0;
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}
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delete [] id_temp;
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int n = strlen(arg[1]) + 1;
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id_temp = new char[n];
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strcpy(id_temp,arg[1]);
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int icompute = modify->find_compute(id_temp);
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if (icompute < 0) error->all("Could not find fix_modify temp ID");
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temperature = modify->compute[icompute];
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if (temperature->tempflag == 0)
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error->all("Fix_modify temp ID does not compute temperature");
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if (temperature->igroup != 0 && comm->me == 0)
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error->warning("Temperature for NPT is not for group all");
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if (strcmp(temperature->style,"region") == 0 && comm->me == 0)
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error->warning("Temperature for NPT is style region");
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// reset id_pre of pressure to new temp ID
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icompute = modify->find_compute(id_press);
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if (icompute < 0) error->all("Press ID for fix npt does not exist");
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delete [] modify->compute[icompute]->id_pre;
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modify->compute[icompute]->id_pre = new char[n];
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strcpy(modify->compute[icompute]->id_pre,id_temp);
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return 2;
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} else if (strcmp(arg[0],"press") == 0) {
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if (narg < 2) error->all("Illegal fix_modify command");
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if (pflag) {
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modify->delete_compute(id_press);
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pflag = 0;
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}
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delete [] id_press;
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int n = strlen(arg[1]) + 1;
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id_press = new char[n];
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strcpy(id_press,arg[1]);
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int icompute = modify->find_compute(id_press);
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if (icompute < 0) error->all("Could not find fix_modify press ID");
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pressure = modify->compute[icompute];
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if (pressure->pressflag == 0)
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error->all("Fix_modify press ID does not compute pressure");
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return 2;
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}
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return 0;
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@ -708,27 +809,19 @@ int FixNPT::modify_param(int narg, char **arg)
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/* ---------------------------------------------------------------------- */
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int FixNPT::thermo_fields(int n, int *flags, char **keywords)
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{
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if (n == 0) return 1;
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flags[0] = 3;
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strcpy(keywords[0],"EngNPT");
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return 1;
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}
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/* ---------------------------------------------------------------------- */
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int FixNPT::thermo_compute(double *values)
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double FixNPT::thermo(int n)
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{
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double ke = temperature->dof * boltz * t_target;
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double keplus = atom->natoms * boltz * t_target;
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double volume = domain->xprd * domain->yprd * domain->zprd;
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int pdim = p_flag[0] + p_flag[1] + p_flag[2];
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values[0] = ke * (eta + 0.5*eta_dot*eta_dot/(t_freq*t_freq));
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double energy = ke * (eta + 0.5*eta_dot*eta_dot/(t_freq*t_freq));
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for (int i = 0; i < 3; i++)
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if (p_freq[i] > 0.0)
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values[0] += 0.5*keplus*omega_dot[i]*omega_dot[i] /
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energy += 0.5*keplus*omega_dot[i]*omega_dot[i] /
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(p_freq[i]*p_freq[i]) + p_target[i]*(volume-vol0) / (pdim*nktv2p);
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return 1;
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if (n == 0) return energy;
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else return 0.0;
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}
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