git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3950 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -8,6 +8,7 @@ if (test $1 = 1) then
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cp atom_vec_ellipsoid.cpp ..
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cp atom_vec_ellipsoid.cpp ..
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cp compute_erotate_asphere.cpp ..
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cp compute_erotate_asphere.cpp ..
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cp compute_temp_asphere.cpp ..
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cp compute_temp_asphere.cpp ..
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cp fix_nph_asphere.cpp ..
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cp fix_npt_asphere.cpp ..
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cp fix_npt_asphere.cpp ..
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cp fix_nve_asphere.cpp ..
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cp fix_nve_asphere.cpp ..
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cp fix_nvt_asphere.cpp ..
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cp fix_nvt_asphere.cpp ..
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@ -17,6 +18,7 @@ if (test $1 = 1) then
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cp atom_vec_ellipsoid.h ..
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cp atom_vec_ellipsoid.h ..
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cp compute_erotate_asphere.h ..
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cp compute_erotate_asphere.h ..
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cp compute_temp_asphere.h ..
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cp compute_temp_asphere.h ..
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cp fix_nph_asphere.h ..
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cp fix_npt_asphere.h ..
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cp fix_npt_asphere.h ..
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cp fix_nve_asphere.h ..
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cp fix_nve_asphere.h ..
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cp fix_nvt_asphere.h ..
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cp fix_nvt_asphere.h ..
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@ -28,6 +30,7 @@ elif (test $1 = 0) then
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rm ../atom_vec_ellipsoid.cpp
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rm ../atom_vec_ellipsoid.cpp
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rm ../compute_erotate_asphere.cpp
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rm ../compute_erotate_asphere.cpp
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rm ../compute_temp_asphere.cpp
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rm ../compute_temp_asphere.cpp
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rm ../fix_nph_asphere.cpp
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rm ../fix_npt_asphere.cpp
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rm ../fix_npt_asphere.cpp
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rm ../fix_nve_asphere.cpp
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rm ../fix_nve_asphere.cpp
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rm ../fix_nvt_asphere.cpp
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rm ../fix_nvt_asphere.cpp
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@ -37,6 +40,7 @@ elif (test $1 = 0) then
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rm ../atom_vec_ellipsoid.h
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rm ../atom_vec_ellipsoid.h
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rm ../compute_erotate_asphere.h
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rm ../compute_erotate_asphere.h
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rm ../compute_temp_asphere.h
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rm ../compute_temp_asphere.h
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rm ../fix_nph_asphere.h
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rm ../fix_npt_asphere.h
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rm ../fix_npt_asphere.h
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rm ../fix_nve_asphere.h
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rm ../fix_nve_asphere.h
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rm ../fix_nvt_asphere.h
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rm ../fix_nvt_asphere.h
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67
src/ASPHERE/fix_nph_asphere.cpp
Normal file
67
src/ASPHERE/fix_nph_asphere.cpp
Normal file
@ -0,0 +1,67 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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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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certain rights in this software. This software is distributed under
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the GNU General Public License.
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|
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "string.h"
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#include "fix_nph_asphere.h"
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#include "modify.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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FixNPHAsphere::FixNPHAsphere(LAMMPS *lmp, int narg, char **arg) :
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FixNHAsphere(lmp, narg, arg)
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{
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if (tstat_flag)
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error->all("Temperature control can not be used with fix nph/asphere");
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if (!pstat_flag)
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error->all("Pressure control must be used with fix nph/asphere");
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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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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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newarg[2] = (char *) "temp/asphere";
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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] = (char *) "all";
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newarg[2] = (char *) "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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}
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36
src/ASPHERE/fix_nph_asphere.h
Normal file
36
src/ASPHERE/fix_nph_asphere.h
Normal file
@ -0,0 +1,36 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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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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|
certain rights in this software. This software is distributed under
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|
the GNU General Public License.
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|
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#ifdef FIX_CLASS
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FixStyle(nph/asphere,FixNPHAsphere)
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#else
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#ifndef LMP_FIX_NPH_ASPHERE_H
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#define LMP_FIX_NPH_ASPHERE_H
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#include "fix_nh_asphere.h"
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namespace LAMMPS_NS {
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class FixNPHAsphere : public FixNHAsphere {
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public:
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FixNPHAsphere(class LAMMPS *, int, char **);
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~FixNPHAsphere() {}
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};
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}
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#endif
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#endif
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@ -11,375 +11,57 @@
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See the README file in the top-level LAMMPS directory.
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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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/* ----------------------------------------------------------------------
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Contributing author: Mike Brown (SNL)
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------------------------------------------------------------------------- */
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#include "string.h"
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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_asphere.h"
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#include "fix_npt_asphere.h"
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#include "math_extra.h"
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#include "modify.h"
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#include "atom.h"
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#include "atom_vec.h"
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#include "force.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 "domain.h"
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#include "memory.h"
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#include "error.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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using namespace LAMMPS_NS;
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enum{NOBIAS,BIAS};
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/* ---------------------------------------------------------------------- */
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/* ---------------------------------------------------------------------- */
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FixNPTAsphere::FixNPTAsphere(LAMMPS *lmp, int narg, char **arg) :
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FixNPTAsphere::FixNPTAsphere(LAMMPS *lmp, int narg, char **arg) :
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FixNPT(lmp, narg, arg)
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FixNHAsphere(lmp, narg, arg)
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{
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{
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inertia =
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if (!tstat_flag)
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memory->create_2d_double_array(atom->ntypes+1,3,"fix_npt_asphere:inertia");
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error->all("Temperature control must be used with fix npt/asphere");
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if (!pstat_flag)
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error->all("Pressure control must be used with fix npt/asphere");
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// error checks
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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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if (!atom->quat_flag || !atom->angmom_flag || !atom->torque_flag ||
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int n = strlen(id) + 6;
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!atom->avec->shape_type)
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id_temp = new char[n];
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error->all("Fix npt/asphere requires atom attributes "
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strcpy(id_temp,id);
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"quat, angmom, torque, shape");
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strcat(id_temp,"_temp");
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if (atom->radius_flag || atom->rmass_flag)
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error->all("Fix npt/asphere cannot be used with atom attributes "
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char **newarg = new char*[3];
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"diameter or rmass");
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newarg[0] = id_temp;
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}
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newarg[1] = (char *) "all";
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newarg[2] = (char *) "temp/asphere";
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/* ---------------------------------------------------------------------- */
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modify->add_compute(3,newarg);
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FixNPTAsphere::~FixNPTAsphere()
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delete [] newarg;
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{
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tflag = 1;
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memory->destroy_2d_double_array(inertia);
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}
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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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/* ---------------------------------------------------------------------- */
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// pass id_temp as 4th arg to pressure constructor
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void FixNPTAsphere::init()
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n = strlen(id) + 7;
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{
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id_press = new char[n];
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// check that all particles are finite-size
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strcpy(id_press,id);
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// no point particles allowed, spherical is OK
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strcat(id_press,"_press");
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double **shape = atom->shape;
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newarg = new char*[4];
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int *type = atom->type;
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newarg[0] = id_press;
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int *mask = atom->mask;
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newarg[1] = (char *) "all";
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int nlocal = atom->nlocal;
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newarg[2] = (char *) "pressure";
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if (igroup == atom->firstgroup) nlocal = atom->nfirst;
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newarg[3] = id_temp;
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modify->add_compute(4,newarg);
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for (int i = 0; i < nlocal; i++)
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delete [] newarg;
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if (mask[i] & groupbit)
|
pflag = 1;
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if (shape[type[i]][0] == 0.0)
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error->one("Fix nvt/asphere requires extended particles");
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FixNPT::init();
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calculate_inertia();
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}
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/* ---------------------------------------------------------------------- */
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void FixNPTAsphere::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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|
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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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|
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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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|
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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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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);
|
|
||||||
|
|
||||||
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);
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
|
||||||
principal moments of inertia for ellipsoids
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
void FixNPTAsphere::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]);
|
|
||||||
}
|
|
||||||
}
|
}
|
||||||
|
|||||||
@ -20,26 +20,14 @@ FixStyle(npt/asphere,FixNPTAsphere)
|
|||||||
#ifndef LMP_FIX_NPT_ASPHERE_H
|
#ifndef LMP_FIX_NPT_ASPHERE_H
|
||||||
#define LMP_FIX_NPT_ASPHERE_H
|
#define LMP_FIX_NPT_ASPHERE_H
|
||||||
|
|
||||||
#include "fix_npt.h"
|
#include "fix_nh_asphere.h"
|
||||||
|
|
||||||
namespace LAMMPS_NS {
|
namespace LAMMPS_NS {
|
||||||
|
|
||||||
class FixNPTAsphere : public FixNPT {
|
class FixNPTAsphere : public FixNHAsphere {
|
||||||
public:
|
public:
|
||||||
FixNPTAsphere(class LAMMPS *, int, char **);
|
FixNPTAsphere(class LAMMPS *, int, char **);
|
||||||
~FixNPTAsphere();
|
~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();
|
|
||||||
};
|
};
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|||||||
@ -11,324 +11,38 @@
|
|||||||
See the README file in the top-level LAMMPS directory.
|
See the README file in the top-level LAMMPS directory.
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
|
||||||
Contributing author: Mike Brown (SNL)
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
#include "string.h"
|
#include "string.h"
|
||||||
#include "stdlib.h"
|
|
||||||
#include "math.h"
|
|
||||||
#include "fix_nvt_asphere.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 "group.h"
|
||||||
#include "update.h"
|
|
||||||
#include "modify.h"
|
#include "modify.h"
|
||||||
#include "compute.h"
|
|
||||||
#include "memory.h"
|
|
||||||
#include "error.h"
|
#include "error.h"
|
||||||
|
|
||||||
using namespace LAMMPS_NS;
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
enum{NOBIAS,BIAS};
|
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
FixNVTAsphere::FixNVTAsphere(LAMMPS *lmp, int narg, char **arg) :
|
FixNVTAsphere::FixNVTAsphere(LAMMPS *lmp, int narg, char **arg) :
|
||||||
FixNVT(lmp, narg, arg)
|
FixNHAsphere(lmp, narg, arg)
|
||||||
{
|
{
|
||||||
inertia =
|
if (!tstat_flag)
|
||||||
memory->create_2d_double_array(atom->ntypes+1,3,"fix_nvt_asphere:inertia");
|
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 ||
|
int n = strlen(id) + 6;
|
||||||
!atom->avec->shape_type)
|
id_temp = new char[n];
|
||||||
error->all("Fix nvt/asphere requires atom attributes "
|
strcpy(id_temp,id);
|
||||||
"quat, angmom, torque, shape");
|
strcat(id_temp,"_temp");
|
||||||
if (atom->radius_flag || atom->rmass_flag)
|
|
||||||
error->all("Fix nvt/asphere cannot be used with atom attributes "
|
char **newarg = new char*[3];
|
||||||
"diameter or rmass");
|
newarg[0] = id_temp;
|
||||||
}
|
newarg[1] = group->names[igroup];
|
||||||
|
newarg[2] = (char *) "temp/asphere";
|
||||||
/* ---------------------------------------------------------------------- */
|
|
||||||
|
modify->add_compute(3,newarg);
|
||||||
FixNVTAsphere::~FixNVTAsphere()
|
delete [] newarg;
|
||||||
{
|
tflag = 1;
|
||||||
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);
|
|
||||||
|
|
||||||
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);
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
|
||||||
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]);
|
|
||||||
}
|
|
||||||
}
|
}
|
||||||
|
|||||||
@ -20,25 +20,14 @@ FixStyle(nvt/asphere,FixNVTAsphere)
|
|||||||
#ifndef LMP_FIX_NVT_ASPHERE_H
|
#ifndef LMP_FIX_NVT_ASPHERE_H
|
||||||
#define LMP_FIX_NVT_ASPHERE_H
|
#define LMP_FIX_NVT_ASPHERE_H
|
||||||
|
|
||||||
#include "fix_nvt.h"
|
#include "fix_nh_asphere.h"
|
||||||
|
|
||||||
namespace LAMMPS_NS {
|
namespace LAMMPS_NS {
|
||||||
|
|
||||||
class FixNVTAsphere : public FixNVT {
|
class FixNVTAsphere : public FixNHAsphere {
|
||||||
public:
|
public:
|
||||||
FixNVTAsphere(class LAMMPS *, int, char **);
|
FixNVTAsphere(class LAMMPS *, int, char **);
|
||||||
~FixNVTAsphere();
|
~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();
|
|
||||||
};
|
};
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|||||||
Reference in New Issue
Block a user