forked from lijiext/lammps
Commit Julien 2 08/23/17
- reorganized includes - start work on magneto-mechanic potential (adding function) - renamed fix_nve_spin into fix_integration_spin
This commit is contained in:
julient31
parent
f5ff30df83
commit
3de0cf5ab4
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@ -84,11 +84,11 @@ fix 1 all force/spin zeeman 10.0 0.0 0.0 1.0
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#Fix Langevin spins (merging damping and temperature)
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#Temp | Alpha_trans | Alpha_long | Seed
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#fix 2 all langevin/spin 0.0 0.1 0.0 21
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fix 2 all langevin/spin 1.0 0.1 0.0 21
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#fix 2 all langevin/spin 0.0 0.0 0.0 21
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#fix 2 all langevin/spin 1.0 0.1 0.0 21
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fix 2 all langevin/spin 0.0 0.0 0.0 21
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#Magnetic integration fix
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fix 3 all nve/spin mpi
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fix 3 all integration/spin mpi
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#compute real time, total magnetization, magnetic energy, and spin temperature
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#Iteration | Time | Mx | My | Mz | |M| | Em | Tm
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@ -96,7 +96,7 @@ compute mag all compute/spin
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fix outmag all ave/time 1 1 10 c_mag[1] c_mag[2] c_mag[3] c_mag[4] c_mag[5] c_mag[6] c_mag[7] file mag_Co_nodamp.dat format %20.16g
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#Setting the timestep for the simulation (in ps)
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timestep 0.00001
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timestep 0.0001
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##################
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#######run########
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@ -106,6 +106,6 @@ timestep 0.00001
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dump 1 all custom 100 dump_spin_MM.lammpstrj type x y z spx spy spz
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#Running the simulations for N timesteps
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run 10000
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run 100000
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#run 1
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@ -14,14 +14,14 @@
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#include <math.h>
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#include <stdlib.h>
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#include <string.h>
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#include "atom_vec_spin.h"
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#include "atom.h"
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#include "atom_vec_spin.h"
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#include "comm.h"
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#include "domain.h"
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#include "modify.h"
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#include "error.h"
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#include "fix.h"
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#include "memory.h"
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#include "error.h"
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#include "modify.h"
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using namespace LAMMPS_NS;
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@ -13,16 +13,16 @@
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#include <mpi.h>
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#include <string.h>
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#include "compute_spin.h"
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#include "atom.h"
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#include "update.h"
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#include "modify.h"
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#include "compute_spin.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 "force.h"
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#include "math_special.h"
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#include "math_const.h"
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#include "force.h"
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#include "memory.h"
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#include "modify.h"
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#include "update.h"
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using namespace LAMMPS_NS;
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using namespace MathSpecial;
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@ -15,18 +15,19 @@
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#include <stdio.h>
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#include <stdlib.h>
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#include <string.h>
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#include "fix_force_spin.h"
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#include "atom.h"
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#include "update.h"
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#include "domain.h"
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#include "respa.h"
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#include "modify.h"
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#include "input.h"
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#include "variable.h"
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#include "math_const.h"
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#include "error.h"
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#include "fix_force_spin.h"
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#include "force.h"
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#include "input.h"
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#include "math_const.h"
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#include "memory.h"
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#include "modify.h"
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#include "respa.h"
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#include "update.h"
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#include "variable.h"
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using namespace LAMMPS_NS;
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using namespace FixConst;
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@ -14,27 +14,26 @@
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#include <math.h>
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#include <stdio.h>
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#include <string.h>
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#include "fix_nve_spin.h"
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#include "atom.h"
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#include "atom_vec.h"
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#include "update.h"
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#include "respa.h"
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#include "force.h"
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#include "error.h"
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#include "fix_force_spin.h"
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#include "fix_integration_spin.h"
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#include "fix_langevin_spin.h"
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#include "force.h"
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#include "math_vector.h"
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#include "math_extra.h"
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#include "math_const.h"
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#include "memory.h"
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#include "modify.h"
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//Add headers (see delete later)
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#include "neighbor.h"
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#include "neigh_list.h"
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#include "pair.h"
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#include "pair_spin.h"
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#include "memory.h"
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#include "fix_force_spin.h"
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#include "fix_langevin_spin.h"
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#include "pair_hybrid.h"
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#include "pair_spin.h"
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#include "respa.h"
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#include "update.h"
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using namespace LAMMPS_NS;
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using namespace FixConst;
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@ -45,11 +44,11 @@ enum{NONE,SPIN};
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/* ---------------------------------------------------------------------- */
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FixNVESpin::FixNVESpin(LAMMPS *lmp, int narg, char **arg) :
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FixIntegrationSpin::FixIntegrationSpin(LAMMPS *lmp, int narg, char **arg) :
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FixNVE(lmp, narg, arg)
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{
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if (narg != 4) error->all(FLERR,"Illegal fix nve/spin command");
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if (narg != 4) error->all(FLERR,"Illegal fix integration/spin command");
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time_integrate = 1;
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@ -57,18 +56,18 @@ FixNVESpin::FixNVESpin(LAMMPS *lmp, int narg, char **arg) :
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mpi_flag = NONE;
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int iarg = 2;
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if (strcmp(arg[iarg],"nve/spin") == 0) {
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if (strcmp(arg[iarg],"integration/spin") == 0) {
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extra = SPIN;
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if (strcmp(arg[iarg+1],"serial") == 0){
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mpi_flag = 0;
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} else if (strcmp(arg[iarg+1],"mpi") == 0) {
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mpi_flag = 1;
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} else error->all(FLERR,"Illegal fix nve/spin command");
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} else error->all(FLERR,"Illegal fix nve/spin command");
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} else error->all(FLERR,"Illegal fix integration/spin command");
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} else error->all(FLERR,"Illegal fix integration/spin command");
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// error checks
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if (extra == SPIN && !atom->mumag_flag)
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error->all(FLERR,"Fix nve/spin requires spin attribute mumag");
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error->all(FLERR,"Fix integration/spin requires spin attribute mumag");
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exch_flag = dmi_flag = me_flag = 0;
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zeeman_flag = aniso_flag = 0;
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@ -80,7 +79,7 @@ FixNVESpin::FixNVESpin(LAMMPS *lmp, int narg, char **arg) :
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}
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/* ---------------------------------------------------------------------- */
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FixNVESpin::~FixNVESpin(){
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FixIntegrationSpin::~FixIntegrationSpin(){
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//delete lockpairspin;
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//delete lockforcespin;
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memory->destroy(xi);
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@ -89,9 +88,6 @@ FixNVESpin::~FixNVESpin(){
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memory->destroy(rsec);
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memory->destroy(seci);
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#if defined SECTOR_PRINT
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fclose(file_sect);
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#endif
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memory->destroy(spi);
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memory->destroy(spj);
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memory->destroy(fmi);
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@ -100,20 +96,20 @@ FixNVESpin::~FixNVESpin(){
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/* ---------------------------------------------------------------------- */
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void FixNVESpin::init()
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void FixIntegrationSpin::init()
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{
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FixNVE::init();
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dts = update->dt;
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memory->create(xi,3,"nves:xi");
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memory->create(sec,3,"nves:sec");
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memory->create(rsec,3,"nves:rsec");
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memory->create(seci,3,"nves:seci");
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memory->create(xi,3,"integrations:xi");
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memory->create(sec,3,"integrations:sec");
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memory->create(rsec,3,"integrations:rsec");
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memory->create(seci,3,"integrations:seci");
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memory->create(spi,3,"nves:spi");
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memory->create(spj,3,"nves:spj");
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memory->create(fmi,3,"nves:fmi");
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memory->create(fmj,3,"nves:fmj");
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memory->create(spi,3,"integrations:spi");
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memory->create(spj,3,"integrations:spj");
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memory->create(fmi,3,"integrations:fmi");
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memory->create(fmj,3,"integrations:fmj");
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if (strstr(force->pair_style,"pair/spin")) {
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@ -127,7 +123,7 @@ void FixNVESpin::init()
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lockpairspin = (PairSpin *) lockhybrid->styles[ipair];
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}
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}
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} else error->all(FLERR,"Illegal fix nve/spin command");
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} else error->all(FLERR,"Illegal fix integration/spin command");
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// check errors, and handle simple hybrid (not overlay)
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@ -168,24 +164,11 @@ void FixNVESpin::init()
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sectoring();
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}
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#if defined SECTOR_PRINT
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file_sect=fopen("sectoring.lammpstrj", "w");
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fprintf(file_sect,"ITEM: TIMESTEP\n");
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fprintf(file_sect,"%g\n",0.0);
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fprintf(file_sect,"ITEM: NUMBER OF ATOMS\n");
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//int natoms = atom->natoms;
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int natoms = atom->nlocal;
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fprintf(file_sect,"%d\n",natoms);
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fprintf(file_sect,"ITEM: BOX BOUNDS\n");
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for(int d=0; d<3; d++) fprintf(file_sect,"%lf %lf\n",domain->boxlo[d],domain->boxhi[d]);
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fprintf(file_sect,"ITEM: ATOMS type x y z vx vy vz\n");
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#endif
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}
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/* ---------------------------------------------------------------------- */
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void FixNVESpin::initial_integrate(int vflag)
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void FixIntegrationSpin::initial_integrate(int vflag)
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{
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double dtfm,msq,scale,fm2,fmsq,sp2,spsq,energy;
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double cp[3],g[3];
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@ -260,7 +243,7 @@ void FixNVESpin::initial_integrate(int vflag)
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ComputeInteractionsSpin(i);
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AdvanceSingleSpin(i,0.5*dts,sp,fm);
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}
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} else error->all(FLERR,"Illegal fix nve/spin command");
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} else error->all(FLERR,"Illegal fix integration/spin command");
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}
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// update half x for all particles
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@ -272,28 +255,24 @@ void FixNVESpin::initial_integrate(int vflag)
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixIntegrationSpin::ComputeMMforce()
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{
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const int nlocal = atom->nlocal;
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int i,j,jj,inum,jnum,itype,jtype;
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int *ilist,*jlist,*numneigh,**firstneigh;
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double **x = atom->x;
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double **f = atom->f;
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double **sp = atom->sp;
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const int newton_pair = force->newton_pair;
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#if defined SECTOR_PRINT
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int my_rank;
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MPI_Comm_rank(world, &my_rank);
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if (my_rank == 0) {
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for (int j = 0; j < nsectors; j++) {
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for (int i = 0; i < nlocal; i++) {
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xi[0] = x[i][0];
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xi[1] = x[i][1];
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xi[2] = x[i][2];
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nseci = coords2sector(xi);
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if (j != nseci) continue;
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fprintf(file_sect,"%d %lf %lf %lf %lf %lf %lf\n",j,xi[0],xi[1],xi[2],0.0,0.0,1.0);
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}
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}
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}
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#endif
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}
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/* ---------------------------------------------------------------------- */
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void FixNVESpin::ComputeInteractionsSpin(int ii)
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void FixIntegrationSpin::ComputeInteractionsSpin(int ii)
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{
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const int nlocal = atom->nlocal;
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@ -403,7 +382,7 @@ void FixNVESpin::ComputeInteractionsSpin(int ii)
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locklangevinspin->add_temperature(fmi);
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}
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// replace the force by its new value
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// replace the magnetic force by its new value
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fm[i][0] = fmi[0];
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fm[i][1] = fmi[1];
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fm[i][2] = fmi[2];
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@ -411,7 +390,7 @@ void FixNVESpin::ComputeInteractionsSpin(int ii)
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}
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/* ---------------------------------------------------------------------- */
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void FixNVESpin::sectoring()
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void FixIntegrationSpin::sectoring()
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{
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double sublo[3],subhi[3];
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double* sublotmp = domain->sublo;
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@ -464,7 +443,7 @@ void FixNVESpin::sectoring()
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}
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/* ---------------------------------------------------------------------- */
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int FixNVESpin::coords2sector(double *xi)
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int FixIntegrationSpin::coords2sector(double *xi)
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{
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int nseci;
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double sublo[3];
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@ -489,7 +468,7 @@ int FixNVESpin::coords2sector(double *xi)
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/* ---------------------------------------------------------------------- */
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void FixNVESpin::AdvanceSingleSpin(int i, double dts, double **sp, double **fm)
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void FixIntegrationSpin::AdvanceSingleSpin(int i, double dts, double **sp, double **fm)
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{
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double dtfm,msq,scale,fm2,fmsq,sp2,spsq,energy;
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double cp[3],g[3];
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@ -530,7 +509,7 @@ void FixNVESpin::AdvanceSingleSpin(int i, double dts, double **sp, double **fm)
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/* ---------------------------------------------------------------------- */
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void FixNVESpin::final_integrate()
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void FixIntegrationSpin::final_integrate()
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{
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double dtfm,msq,scale,fm2,fmsq,energy;
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double cp[3],g[3];
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@ -13,7 +13,7 @@
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#ifdef FIX_CLASS
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FixStyle(nve/spin,FixNVESpin)
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FixStyle(integration/spin,FixIntegrationSpin)
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#else
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@ -24,18 +24,18 @@ FixStyle(nve/spin,FixNVESpin)
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namespace LAMMPS_NS {
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class FixNVESpin : public FixNVE {
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class FixIntegrationSpin : public FixNVE {
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public:
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FixNVESpin(class LAMMPS *, int, char **);
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virtual ~FixNVESpin();
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FixIntegrationSpin(class LAMMPS *, int, char **);
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virtual ~FixIntegrationSpin();
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void init();
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virtual void initial_integrate(int);
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void AdvanceSingleSpin(int, double, double **, double **);
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virtual void final_integrate();
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void ComputeSpinInteractions();
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void ComputeInteractionsSpin(int);
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void ComputeMMforce();
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void sectoring();
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int coords2sector(double *);
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@ -59,10 +59,6 @@ class FixNVESpin : public FixNVE {
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int *sec, *seci;
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double *rsec;
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//#define SECTOR_PRINT
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#if defined SECTOR_PRINT
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FILE* file_sect=NULL;
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#endif
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};
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}
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@ -20,26 +20,27 @@
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#include <math.h>
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#include <string.h>
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#include <stdlib.h>
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#include "fix_langevin_spin.h"
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#include "math_extra.h"
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#include "atom.h"
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#include "atom_vec_ellipsoid.h"
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#include "force.h"
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#include "update.h"
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#include "modify.h"
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#include "comm.h"
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#include "compute.h"
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#include "domain.h"
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#include "error.h"
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#include "fix_langevin_spin.h"
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#include "force.h"
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#include "group.h"
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#include "input.h"
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#include "math_const.h"
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#include "math_extra.h"
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#include "memory.h"
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#include "modify.h"
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#include "random_mars.h"
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#include "random_park.h"
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#include "region.h"
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#include "respa.h"
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#include "comm.h"
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#include "input.h"
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#include "update.h"
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#include "variable.h"
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#include "random_mars.h"
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#include "memory.h"
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#include "error.h"
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#include "group.h"
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#include "math_const.h"
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#include "random_park.h"
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using namespace LAMMPS_NS;
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using namespace FixConst;
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@ -13,20 +13,19 @@
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#include <math.h>
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#include <stdlib.h>
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#include "pair_spin.h"
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#include "atom.h"
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#include "neighbor.h"
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#include "neigh_list.h"
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#include "comm.h"
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#include "force.h"
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#include "memory.h"
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#include "math_const.h"
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#include "error.h"
|
||||
#include "update.h"
|
||||
#include <string.h>
|
||||
|
||||
//Add. lib. for full neighb. list
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
#include "neigh_request.h"
|
||||
#include "math_const.h"
|
||||
#include "memory.h"
|
||||
#include "pair_spin.h"
|
||||
#include "update.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace MathConst;
|
||||
|
|
|
|||
|
|
@ -31,7 +31,7 @@ class PairHybrid : public Pair {
|
|||
friend class FixOMP;
|
||||
friend class Force;
|
||||
friend class Respa;
|
||||
friend class FixNVESpin;
|
||||
friend class FixIntegrationSpin;
|
||||
friend class Info;
|
||||
public:
|
||||
PairHybrid(class LAMMPS *);
|
||||
|
|
|
|||
Loading…
Reference in New Issue