From 02ac8178c5b0cc1c28722d22bc45ae16baf6cf97 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 2 Apr 2010 16:53:02 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3950 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/ASPHERE/Install.sh | 4 + src/ASPHERE/fix_nph_asphere.cpp | 67 ++++++ src/ASPHERE/fix_nph_asphere.h | 36 +++ src/ASPHERE/fix_npt_asphere.cpp | 390 +++----------------------------- src/ASPHERE/fix_npt_asphere.h | 18 +- src/ASPHERE/fix_nvt_asphere.cpp | 322 ++------------------------ src/ASPHERE/fix_nvt_asphere.h | 17 +- 7 files changed, 167 insertions(+), 687 deletions(-) create mode 100644 src/ASPHERE/fix_nph_asphere.cpp create mode 100644 src/ASPHERE/fix_nph_asphere.h diff --git a/src/ASPHERE/Install.sh b/src/ASPHERE/Install.sh index ccb5f781cb..f39a0604ec 100644 --- a/src/ASPHERE/Install.sh +++ b/src/ASPHERE/Install.sh @@ -8,6 +8,7 @@ if (test $1 = 1) then cp atom_vec_ellipsoid.cpp .. cp compute_erotate_asphere.cpp .. cp compute_temp_asphere.cpp .. + cp fix_nph_asphere.cpp .. cp fix_npt_asphere.cpp .. cp fix_nve_asphere.cpp .. cp fix_nvt_asphere.cpp .. @@ -17,6 +18,7 @@ if (test $1 = 1) then cp atom_vec_ellipsoid.h .. cp compute_erotate_asphere.h .. cp compute_temp_asphere.h .. + cp fix_nph_asphere.h .. cp fix_npt_asphere.h .. cp fix_nve_asphere.h .. cp fix_nvt_asphere.h .. @@ -28,6 +30,7 @@ elif (test $1 = 0) then rm ../atom_vec_ellipsoid.cpp rm ../compute_erotate_asphere.cpp rm ../compute_temp_asphere.cpp + rm ../fix_nph_asphere.cpp rm ../fix_npt_asphere.cpp rm ../fix_nve_asphere.cpp rm ../fix_nvt_asphere.cpp @@ -37,6 +40,7 @@ elif (test $1 = 0) then rm ../atom_vec_ellipsoid.h rm ../compute_erotate_asphere.h rm ../compute_temp_asphere.h + rm ../fix_nph_asphere.h rm ../fix_npt_asphere.h rm ../fix_nve_asphere.h rm ../fix_nvt_asphere.h diff --git a/src/ASPHERE/fix_nph_asphere.cpp b/src/ASPHERE/fix_nph_asphere.cpp new file mode 100644 index 0000000000..025137def2 --- /dev/null +++ b/src/ASPHERE/fix_nph_asphere.cpp @@ -0,0 +1,67 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "string.h" +#include "fix_nph_asphere.h" +#include "modify.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +FixNPHAsphere::FixNPHAsphere(LAMMPS *lmp, int narg, char **arg) : + FixNHAsphere(lmp, narg, arg) +{ + if (tstat_flag) + error->all("Temperature control can not be used with fix nph/asphere"); + if (!pstat_flag) + error->all("Pressure control must be used with fix nph/asphere"); + + // create a new compute temp style + // id = fix-ID + temp + // compute group = all since pressure is always global (group all) + // and thus its KE/temperature contribution should use group all + + int n = strlen(id) + 6; + id_temp = new char[n]; + strcpy(id_temp,id); + strcat(id_temp,"_temp"); + + char **newarg = new char*[3]; + newarg[0] = id_temp; + newarg[1] = (char *) "all"; + newarg[2] = (char *) "temp/asphere"; + + modify->add_compute(3,newarg); + delete [] newarg; + tflag = 1; + + // create a new compute pressure style + // id = fix-ID + press, compute group = all + // pass id_temp as 4th arg to pressure constructor + + n = strlen(id) + 7; + id_press = new char[n]; + strcpy(id_press,id); + strcat(id_press,"_press"); + + newarg = new char*[4]; + newarg[0] = id_press; + newarg[1] = (char *) "all"; + newarg[2] = (char *) "pressure"; + newarg[3] = id_temp; + modify->add_compute(4,newarg); + delete [] newarg; + pflag = 1; +} diff --git a/src/ASPHERE/fix_nph_asphere.h b/src/ASPHERE/fix_nph_asphere.h new file mode 100644 index 0000000000..87a8b1ce13 --- /dev/null +++ b/src/ASPHERE/fix_nph_asphere.h @@ -0,0 +1,36 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(nph/asphere,FixNPHAsphere) + +#else + +#ifndef LMP_FIX_NPH_ASPHERE_H +#define LMP_FIX_NPH_ASPHERE_H + +#include "fix_nh_asphere.h" + +namespace LAMMPS_NS { + +class FixNPHAsphere : public FixNHAsphere { + public: + FixNPHAsphere(class LAMMPS *, int, char **); + ~FixNPHAsphere() {} +}; + +} + +#endif +#endif diff --git a/src/ASPHERE/fix_npt_asphere.cpp b/src/ASPHERE/fix_npt_asphere.cpp index 9f7233bc46..44ed01ea45 100755 --- a/src/ASPHERE/fix_npt_asphere.cpp +++ b/src/ASPHERE/fix_npt_asphere.cpp @@ -11,375 +11,57 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -/* ---------------------------------------------------------------------- - Contributing author: Mike Brown (SNL) -------------------------------------------------------------------------- */ - #include "string.h" -#include "stdlib.h" -#include "math.h" #include "fix_npt_asphere.h" -#include "math_extra.h" -#include "atom.h" -#include "atom_vec.h" -#include "force.h" -#include "compute.h" -#include "kspace.h" -#include "update.h" -#include "domain.h" -#include "memory.h" +#include "modify.h" #include "error.h" using namespace LAMMPS_NS; -enum{NOBIAS,BIAS}; - /* ---------------------------------------------------------------------- */ FixNPTAsphere::FixNPTAsphere(LAMMPS *lmp, int narg, char **arg) : - FixNPT(lmp, narg, arg) + FixNHAsphere(lmp, narg, arg) { - inertia = - memory->create_2d_double_array(atom->ntypes+1,3,"fix_npt_asphere:inertia"); + if (!tstat_flag) + error->all("Temperature control must be used with fix npt/asphere"); + if (!pstat_flag) + error->all("Pressure control must be used with fix npt/asphere"); - // error checks + // create a new compute temp style + // id = fix-ID + temp + // compute group = all since pressure is always global (group all) + // and thus its KE/temperature contribution should use group all - if (!atom->quat_flag || !atom->angmom_flag || !atom->torque_flag || - !atom->avec->shape_type) - error->all("Fix npt/asphere requires atom attributes " - "quat, angmom, torque, shape"); - if (atom->radius_flag || atom->rmass_flag) - error->all("Fix npt/asphere cannot be used with atom attributes " - "diameter or rmass"); -} - -/* ---------------------------------------------------------------------- */ - -FixNPTAsphere::~FixNPTAsphere() -{ - memory->destroy_2d_double_array(inertia); -} - -/* ---------------------------------------------------------------------- */ - -void FixNPTAsphere::init() -{ - // check that all particles are finite-size - // no point particles allowed, spherical is OK - - double **shape = atom->shape; - int *type = atom->type; - int *mask = atom->mask; - int nlocal = atom->nlocal; - if (igroup == atom->firstgroup) nlocal = atom->nfirst; - - for (int i = 0; i < nlocal; i++) - if (mask[i] & groupbit) - if (shape[type[i]][0] == 0.0) - error->one("Fix nvt/asphere requires extended particles"); - - FixNPT::init(); - calculate_inertia(); -} - -/* ---------------------------------------------------------------------- */ - -void FixNPTAsphere::initial_integrate(int vflag) -{ - int i; - double dtfm; - - 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 (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]); - } - factor_rotate = exp(-dthalf*eta_dot); - - // 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 **x = atom->x; - double **v = atom->v; - double **f = atom->f; - double **quat = atom->quat; - double **angmom = atom->angmom; - double **torque = atom->torque; - double *mass = atom->mass; - int *type = atom->type; - int *mask = atom->mask; - int nlocal = atom->nlocal; - if (igroup == atom->firstgroup) nlocal = atom->nfirst; - - if (which == NOBIAS) { - for (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]; - } - } - } 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]; - } - } - - // set timestep here since dt may have changed or come via rRESPA - - dtq = 0.5 * dtv; - - // update angular momentum by 1/2 step for atoms in group - // update quaternion a full step via Richardson iteration - // returns new normalized quaternion - - for (i = 0; i < nlocal; i++) { - if (mask[i] & groupbit) { - angmom[i][0] = angmom[i][0]*factor_rotate + dtf*torque[i][0]; - angmom[i][1] = angmom[i][1]*factor_rotate + dtf*torque[i][1]; - angmom[i][2] = angmom[i][2]*factor_rotate + dtf*torque[i][2]; - - richardson(quat[i],angmom[i],inertia[type[i]]); - } - } - - // remap simulation box by 1/2 step - // redo KSpace coeffs since volume has changed - - remap(); - if (kspace_flag) force->kspace->setup(); -} - -/* ---------------------------------------------------------------------- */ - -void FixNPTAsphere::final_integrate() -{ - int i; - double dtfm; - - // update v,angmom 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 **angmom = atom->angmom; - double **torque = atom->torque; - double *mass = atom->mass; - int *type = atom->type; - int *mask = atom->mask; - int nlocal = atom->nlocal; - if (igroup == atom->firstgroup) nlocal = atom->nfirst; - - 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]; - angmom[i][0] = (angmom[i][0] + dtf * torque[i][0]) * factor_rotate; - angmom[i][1] = (angmom[i][1] + dtf * torque[i][1]) * factor_rotate; - angmom[i][2] = (angmom[i][2] + dtf * torque[i][2]) * factor_rotate; - } - } - } 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]); - angmom[i][0] = (angmom[i][0] + dtf * torque[i][0]) * factor_rotate; - angmom[i][1] = (angmom[i][1] + dtf * torque[i][1]) * factor_rotate; - angmom[i][2] = (angmom[i][2] + dtf * torque[i][2]) * factor_rotate; - } - } - } - - // compute new T,P - - t_current = temperature->compute_scalar(); - if (press_couple == 0) { - 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; - } -} - -/* ---------------------------------------------------------------------- - Richardson iteration to update quaternion accurately -------------------------------------------------------------------------- */ - -void FixNPTAsphere::richardson(double *q, double *m, double *moments) -{ - // compute omega at 1/2 step from m at 1/2 step and q at 0 - - double w[3]; - omega_from_mq(q,m,moments,w); - - // full update from dq/dt = 1/2 w q - - double wq[4]; - MathExtra::multiply_vec_quat(w,q,wq); - - double qfull[4]; - qfull[0] = q[0] + dtq * wq[0]; - qfull[1] = q[1] + dtq * wq[1]; - qfull[2] = q[2] + dtq * wq[2]; - qfull[3] = q[3] + dtq * wq[3]; - MathExtra::normalize4(qfull); - - // 1st half of update from dq/dt = 1/2 w q - - double qhalf[4]; - qhalf[0] = q[0] + 0.5*dtq * wq[0]; - qhalf[1] = q[1] + 0.5*dtq * wq[1]; - qhalf[2] = q[2] + 0.5*dtq * wq[2]; - qhalf[3] = q[3] + 0.5*dtq * wq[3]; - MathExtra::normalize4(qhalf); - - // re-compute omega at 1/2 step from m at 1/2 step and q at 1/2 step - // recompute wq - - omega_from_mq(qhalf,m,moments,w); - MathExtra::multiply_vec_quat(w,qhalf,wq); - - // 2nd half of update from dq/dt = 1/2 w q - - qhalf[0] += 0.5*dtq * wq[0]; - qhalf[1] += 0.5*dtq * wq[1]; - qhalf[2] += 0.5*dtq * wq[2]; - qhalf[3] += 0.5*dtq * wq[3]; - MathExtra::normalize4(qhalf); - - // corrected Richardson update - - q[0] = 2.0*qhalf[0] - qfull[0]; - q[1] = 2.0*qhalf[1] - qfull[1]; - q[2] = 2.0*qhalf[2] - qfull[2]; - q[3] = 2.0*qhalf[3] - qfull[3]; - MathExtra::normalize4(q); -} - -/* ---------------------------------------------------------------------- - compute omega from angular momentum - w = omega = angular velocity in space frame - wbody = angular velocity in body frame - project space-frame angular momentum onto body axes - and divide by principal moments -------------------------------------------------------------------------- */ - -void FixNPTAsphere::omega_from_mq(double *q, double *m, double *inertia, - double *w) -{ - double rot[3][3]; - MathExtra::quat_to_mat(q,rot); + int n = strlen(id) + 6; + id_temp = new char[n]; + strcpy(id_temp,id); + strcat(id_temp,"_temp"); - double wbody[3]; - MathExtra::transpose_times_column3(rot,m,wbody); - wbody[0] /= inertia[0]; - wbody[1] /= inertia[1]; - wbody[2] /= inertia[2]; - MathExtra::times_column3(rot,wbody,w); -} + char **newarg = new char*[3]; + newarg[0] = id_temp; + newarg[1] = (char *) "all"; + newarg[2] = (char *) "temp/asphere"; + modify->add_compute(3,newarg); + delete [] newarg; + tflag = 1; -/* ---------------------------------------------------------------------- - principal moments of inertia for ellipsoids -------------------------------------------------------------------------- */ + // create a new compute pressure style + // id = fix-ID + press, compute group = all + // pass id_temp as 4th arg to pressure constructor -void FixNPTAsphere::calculate_inertia() -{ - double *mass = atom->mass; - double **shape = atom->shape; + n = strlen(id) + 7; + id_press = new char[n]; + strcpy(id_press,id); + strcat(id_press,"_press"); - for (int i = 1; i <= atom->ntypes; i++) { - inertia[i][0] = 0.2*mass[i] * - (shape[i][1]*shape[i][1]+shape[i][2]*shape[i][2]); - inertia[i][1] = 0.2*mass[i] * - (shape[i][0]*shape[i][0]+shape[i][2]*shape[i][2]); - inertia[i][2] = 0.2*mass[i] * - (shape[i][0]*shape[i][0]+shape[i][1]*shape[i][1]); - } + newarg = new char*[4]; + newarg[0] = id_press; + newarg[1] = (char *) "all"; + newarg[2] = (char *) "pressure"; + newarg[3] = id_temp; + modify->add_compute(4,newarg); + delete [] newarg; + pflag = 1; } diff --git a/src/ASPHERE/fix_npt_asphere.h b/src/ASPHERE/fix_npt_asphere.h index 110977e8ff..fb8f3cf5c2 100755 --- a/src/ASPHERE/fix_npt_asphere.h +++ b/src/ASPHERE/fix_npt_asphere.h @@ -20,26 +20,14 @@ FixStyle(npt/asphere,FixNPTAsphere) #ifndef LMP_FIX_NPT_ASPHERE_H #define LMP_FIX_NPT_ASPHERE_H -#include "fix_npt.h" +#include "fix_nh_asphere.h" namespace LAMMPS_NS { -class FixNPTAsphere : public FixNPT { +class FixNPTAsphere : public FixNHAsphere { public: FixNPTAsphere(class LAMMPS *, int, char **); - ~FixNPTAsphere(); - void init(); - void initial_integrate(int); - void final_integrate(); - - private: - double dtq; - double factor_rotate; - double **inertia; - - void richardson(double *, double *, double *); - void omega_from_mq(double *, double *, double *, double *); - void calculate_inertia(); + ~FixNPTAsphere() {} }; } diff --git a/src/ASPHERE/fix_nvt_asphere.cpp b/src/ASPHERE/fix_nvt_asphere.cpp index d30db19d9e..4137941be9 100755 --- a/src/ASPHERE/fix_nvt_asphere.cpp +++ b/src/ASPHERE/fix_nvt_asphere.cpp @@ -11,324 +11,38 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -/* ---------------------------------------------------------------------- - Contributing author: Mike Brown (SNL) -------------------------------------------------------------------------- */ - #include "string.h" -#include "stdlib.h" -#include "math.h" #include "fix_nvt_asphere.h" -#include "math_extra.h" -#include "atom.h" -#include "atom_vec.h" -#include "force.h" -#include "comm.h" #include "group.h" -#include "update.h" #include "modify.h" -#include "compute.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; -enum{NOBIAS,BIAS}; - /* ---------------------------------------------------------------------- */ FixNVTAsphere::FixNVTAsphere(LAMMPS *lmp, int narg, char **arg) : - FixNVT(lmp, narg, arg) + FixNHAsphere(lmp, narg, arg) { - inertia = - memory->create_2d_double_array(atom->ntypes+1,3,"fix_nvt_asphere:inertia"); + if (!tstat_flag) + error->all("Temperature control must be used with fix nvt/asphere"); + if (pstat_flag) + error->all("Pressure control can not be used with fix nvt/asphere"); - // error checks + // create a new compute temp style + // id = fix-ID + temp - if (!atom->quat_flag || !atom->angmom_flag || !atom->torque_flag || - !atom->avec->shape_type) - error->all("Fix nvt/asphere requires atom attributes " - "quat, angmom, torque, shape"); - if (atom->radius_flag || atom->rmass_flag) - error->all("Fix nvt/asphere cannot be used with atom attributes " - "diameter or rmass"); -} - -/* ---------------------------------------------------------------------- */ - -FixNVTAsphere::~FixNVTAsphere() -{ - memory->destroy_2d_double_array(inertia); -} - -/* ---------------------------------------------------------------------- */ - -void FixNVTAsphere::init() -{ - // check that all particles are finite-size - // no point particles allowed, spherical is OK - - double **shape = atom->shape; - int *type = atom->type; - int *mask = atom->mask; - int nlocal = atom->nlocal; - if (igroup == atom->firstgroup) nlocal = atom->nfirst; - - for (int i = 0; i < nlocal; i++) - if (mask[i] & groupbit) - if (shape[type[i]][0] == 0.0) - error->one("Fix nvt/asphere requires extended particles"); - - FixNVT::init(); - calculate_inertia(); -} - -/* ---------------------------------------------------------------------- */ - -void FixNVTAsphere::initial_integrate(int vflag) -{ - double dtfm; - - double delta = update->ntimestep - update->beginstep; - delta /= update->endstep - update->beginstep; - t_target = t_start + delta * (t_stop-t_start); - - // update eta_dot - - 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; - factor = exp(-dthalf*eta_dot); - - // update v,x,angmom 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 **x = atom->x; - double **v = atom->v; - double **f = atom->f; - double **quat = atom->quat; - double **angmom = atom->angmom; - double **torque = atom->torque; - double *mass = atom->mass; - int *type = atom->type; - int *mask = atom->mask; - int nlocal = atom->nlocal; - if (igroup == atom->firstgroup) nlocal = atom->nfirst; - - // set timestep here since dt may have changed or come via rRESPA - - dtq = 0.5 * dtv; - - if (which == NOBIAS) { - for (int i = 0; i < nlocal; i++) { - if (mask[i] & groupbit) { - dtfm = dtf / mass[type[i]]; - v[i][0] = v[i][0]*factor + dtfm*f[i][0]; - v[i][1] = v[i][1]*factor + dtfm*f[i][1]; - v[i][2] = v[i][2]*factor + dtfm*f[i][2]; - x[i][0] += dtv * v[i][0]; - x[i][1] += dtv * v[i][1]; - x[i][2] += dtv * v[i][2]; - - // update angular momentum by 1/2 step - // update quaternion a full step via Richardson iteration - // returns new normalized quaternion - - angmom[i][0] = angmom[i][0]*factor + dtf*torque[i][0]; - angmom[i][1] = angmom[i][1]*factor + dtf*torque[i][1]; - angmom[i][2] = angmom[i][2]*factor + dtf*torque[i][2]; - - richardson(quat[i],angmom[i],inertia[type[i]]); - } - } - - } else { - double tmp = temperature->compute_scalar(); - for (int 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 + dtfm*f[i][0]; - v[i][1] = v[i][1]*factor + dtfm*f[i][1]; - v[i][2] = v[i][2]*factor + dtfm*f[i][2]; - temperature->restore_bias(i,v[i]); - x[i][0] += dtv * v[i][0]; - x[i][1] += dtv * v[i][1]; - x[i][2] += dtv * v[i][2]; - - // update angular momentum by 1/2 step - // update quaternion a full step via Richardson iteration - // returns new normalized quaternion - - angmom[i][0] = angmom[i][0]*factor + dtf*torque[i][0]; - angmom[i][1] = angmom[i][1]*factor + dtf*torque[i][1]; - angmom[i][2] = angmom[i][2]*factor + dtf*torque[i][2]; - - richardson(quat[i],angmom[i],inertia[type[i]]); - } - } - } -} - -/* ---------------------------------------------------------------------- */ - -void FixNVTAsphere::final_integrate() -{ - double dtfm; - - // update v,angmom 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 **angmom = atom->angmom; - double **torque = atom->torque; - double *mass = atom->mass; - int *type = atom->type; - int *mask = atom->mask; - int nlocal = atom->nlocal; - if (igroup == atom->firstgroup) nlocal = atom->nfirst; - - if (which == NOBIAS) { - for (int i = 0; i < nlocal; i++) { - if (mask[i] & groupbit) { - dtfm = dtf / mass[type[i]] * factor; - v[i][0] = v[i][0]*factor + dtfm*f[i][0]; - v[i][1] = v[i][1]*factor + dtfm*f[i][1]; - v[i][2] = v[i][2]*factor + dtfm*f[i][2]; - angmom[i][0] = (angmom[i][0] + dtf*torque[i][0]) * factor; - angmom[i][1] = (angmom[i][1] + dtf*torque[i][1]) * factor; - angmom[i][2] = (angmom[i][2] + dtf*torque[i][2]) * factor; - } - } - - } else { - double tmp = temperature->compute_scalar(); - for (int i = 0; i < nlocal; i++) { - if (mask[i] & groupbit) { - temperature->remove_bias(i,v[i]); - dtfm = dtf / mass[type[i]] * factor; - v[i][0] = v[i][0]*factor + dtfm*f[i][0]; - v[i][1] = v[i][1]*factor + dtfm*f[i][1]; - v[i][2] = v[i][2]*factor + dtfm*f[i][2]; - temperature->restore_bias(i,v[i]); - angmom[i][0] = (angmom[i][0] + dtf*torque[i][0]) * factor; - angmom[i][1] = (angmom[i][1] + dtf*torque[i][1]) * factor; - angmom[i][2] = (angmom[i][2] + dtf*torque[i][2]) * factor; - } - } - } - - // compute current T - - t_current = temperature->compute_scalar(); - - // update eta_dot - - f_eta = t_freq*t_freq * (t_current/t_target - 1.0); - eta_dot += f_eta*dthalf; - eta_dot *= drag_factor; -} - -/* ---------------------------------------------------------------------- - Richardson iteration to update quaternion accurately -------------------------------------------------------------------------- */ - -void FixNVTAsphere::richardson(double *q, double *m, double *moments) -{ - // compute omega at 1/2 step from m at 1/2 step and q at 0 - - double w[3]; - omega_from_mq(q,m,moments,w); - - // full update from dq/dt = 1/2 w q - - double wq[4]; - MathExtra::multiply_vec_quat(w,q,wq); - - double qfull[4]; - qfull[0] = q[0] + dtq * wq[0]; - qfull[1] = q[1] + dtq * wq[1]; - qfull[2] = q[2] + dtq * wq[2]; - qfull[3] = q[3] + dtq * wq[3]; - MathExtra::normalize4(qfull); - - // 1st half of update from dq/dt = 1/2 w q - - double qhalf[4]; - qhalf[0] = q[0] + 0.5*dtq * wq[0]; - qhalf[1] = q[1] + 0.5*dtq * wq[1]; - qhalf[2] = q[2] + 0.5*dtq * wq[2]; - qhalf[3] = q[3] + 0.5*dtq * wq[3]; - MathExtra::normalize4(qhalf); - - // re-compute omega at 1/2 step from m at 1/2 step and q at 1/2 step - // recompute wq - - omega_from_mq(qhalf,m,moments,w); - MathExtra::multiply_vec_quat(w,qhalf,wq); - - // 2nd half of update from dq/dt = 1/2 w q - - qhalf[0] += 0.5*dtq * wq[0]; - qhalf[1] += 0.5*dtq * wq[1]; - qhalf[2] += 0.5*dtq * wq[2]; - qhalf[3] += 0.5*dtq * wq[3]; - MathExtra::normalize4(qhalf); - - // corrected Richardson update - - q[0] = 2.0*qhalf[0] - qfull[0]; - q[1] = 2.0*qhalf[1] - qfull[1]; - q[2] = 2.0*qhalf[2] - qfull[2]; - q[3] = 2.0*qhalf[3] - qfull[3]; - MathExtra::normalize4(q); -} - -/* ---------------------------------------------------------------------- - compute omega from angular momentum - w = omega = angular velocity in space frame - wbody = angular velocity in body frame - project space-frame angular momentum onto body axes - and divide by principal moments -------------------------------------------------------------------------- */ - -void FixNVTAsphere::omega_from_mq(double *q, double *m, double *inertia, - double *w) -{ - double rot[3][3]; - MathExtra::quat_to_mat(q,rot); + int n = strlen(id) + 6; + id_temp = new char[n]; + strcpy(id_temp,id); + strcat(id_temp,"_temp"); - double wbody[3]; - MathExtra::transpose_times_column3(rot,m,wbody); - wbody[0] /= inertia[0]; - wbody[1] /= inertia[1]; - wbody[2] /= inertia[2]; - MathExtra::times_column3(rot,wbody,w); -} + char **newarg = new char*[3]; + newarg[0] = id_temp; + newarg[1] = group->names[igroup]; + newarg[2] = (char *) "temp/asphere"; -/* ---------------------------------------------------------------------- - principal moments of inertia for ellipsoids -------------------------------------------------------------------------- */ - -void FixNVTAsphere::calculate_inertia() -{ - double *mass = atom->mass; - double **shape = atom->shape; - - for (int i = 1; i <= atom->ntypes; i++) { - inertia[i][0] = 0.2*mass[i] * - (shape[i][1]*shape[i][1]+shape[i][2]*shape[i][2]); - inertia[i][1] = 0.2*mass[i] * - (shape[i][0]*shape[i][0]+shape[i][2]*shape[i][2]); - inertia[i][2] = 0.2*mass[i] * - (shape[i][0]*shape[i][0]+shape[i][1]*shape[i][1]); - } + modify->add_compute(3,newarg); + delete [] newarg; + tflag = 1; } diff --git a/src/ASPHERE/fix_nvt_asphere.h b/src/ASPHERE/fix_nvt_asphere.h index 5ebe635714..59f1111e16 100755 --- a/src/ASPHERE/fix_nvt_asphere.h +++ b/src/ASPHERE/fix_nvt_asphere.h @@ -20,25 +20,14 @@ FixStyle(nvt/asphere,FixNVTAsphere) #ifndef LMP_FIX_NVT_ASPHERE_H #define LMP_FIX_NVT_ASPHERE_H -#include "fix_nvt.h" +#include "fix_nh_asphere.h" namespace LAMMPS_NS { -class FixNVTAsphere : public FixNVT { +class FixNVTAsphere : public FixNHAsphere { public: FixNVTAsphere(class LAMMPS *, int, char **); - ~FixNVTAsphere(); - void init(); - void initial_integrate(int); - void final_integrate(); - - private: - double dtq; - double **inertia; - - void richardson(double *, double *, double *); - void omega_from_mq(double *, double *, double *, double *); - void calculate_inertia(); + ~FixNVTAsphere() {} }; }