forked from lijiext/lammps
Commit JT 062719
- cleaned code and setup LAMMPS format and indentation - added src/min_spin_oso_cg.h/cpp to .gitignore
This commit is contained in:
julient31
parent
2520eab46d
commit
3e8ab7cbb0
|
|
@ -161,6 +161,8 @@
|
|||
/fix_setforce_spin.h
|
||||
/min_spin.cpp
|
||||
/min_spin.h
|
||||
/min_spin_oso_cg.cpp
|
||||
/min_spin_oso_cg.h
|
||||
/neb_spin.cpp
|
||||
/neb_spin.h
|
||||
/pair_spin.cpp
|
||||
|
|
|
|||
|
|
@ -12,9 +12,13 @@
|
|||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ------------------------------------------------------------------------
|
||||
Contributing authors: Julien Tranchida (SNL), Aleksei Ivanov (UI)
|
||||
Contributing authors: Aleksei Ivanov (UI)
|
||||
Julien Tranchida (SNL)
|
||||
|
||||
Please cite the related publication:
|
||||
Ivanov, A. V., Uzdin, V. M., & Jónsson, H. (2019). Fast and Robust
|
||||
Algorithm for the Minimisation of the Energy of Spin Systems. arXiv
|
||||
preprint arXiv:1904.02669.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <mpi.h>
|
||||
|
|
@ -24,6 +28,7 @@
|
|||
#include "min_spin_oso_cg.h"
|
||||
#include "universe.h"
|
||||
#include "atom.h"
|
||||
#include "citeme.h"
|
||||
#include "force.h"
|
||||
#include "update.h"
|
||||
#include "output.h"
|
||||
|
|
@ -36,18 +41,28 @@
|
|||
using namespace LAMMPS_NS;
|
||||
using namespace MathConst;
|
||||
|
||||
static const char cite_minstyle_spin_oso_cg[] =
|
||||
"min_style spin/oso_cg command:\n\n"
|
||||
"@article{ivanov2019fast,\n"
|
||||
"title={Fast and Robust Algorithm for the Minimisation of the Energy of "
|
||||
"Spin Systems},\n"
|
||||
"author={Ivanov, A. V and Uzdin, V. M. and J{\'o}nsson, H.},\n"
|
||||
"journal={arXiv preprint arXiv:1904.02669},\n"
|
||||
"year={2019}\n"
|
||||
"}\n\n";
|
||||
|
||||
// EPS_ENERGY = minimum normalization for energy tolerance
|
||||
|
||||
#define EPS_ENERGY 1.0e-8
|
||||
|
||||
#define DELAYSTEP 5
|
||||
|
||||
void vm3(const double *m, const double *v, double *out);
|
||||
void rodrigues_rotation(const double *upp_tr, double *out);
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
MinSpinOSO_CG::MinSpinOSO_CG(LAMMPS *lmp) : Min(lmp) {}
|
||||
MinSpinOSO_CG::MinSpinOSO_CG(LAMMPS *lmp) : Min(lmp) {
|
||||
if (lmp->citeme) lmp->citeme->add(cite_minstyle_spin_oso_cg);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
|
|
@ -258,22 +273,29 @@ void MinSpinOSO_CG::calc_gradient(double dts)
|
|||
double **sp = atom->sp;
|
||||
double **fm = atom->fm;
|
||||
double tdampx, tdampy, tdampz;
|
||||
|
||||
// loop on all spins on proc.
|
||||
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
|
||||
// calc. damping torque
|
||||
|
||||
tdampx = -alpha_damp*(fm[i][1]*sp[i][2] - fm[i][2]*sp[i][1]);
|
||||
tdampy = -alpha_damp*(fm[i][2]*sp[i][0] - fm[i][0]*sp[i][2]);
|
||||
tdampz = -alpha_damp*(fm[i][0]*sp[i][1] - fm[i][1]*sp[i][0]);
|
||||
|
||||
// calculate gradients
|
||||
|
||||
g[3 * i + 0] = -tdampz * dts;
|
||||
g[3 * i + 1] = tdampy * dts;
|
||||
g[3 * i + 2] = -tdampx * dts;
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
search direction
|
||||
---------------------------------------------------------------------- */
|
||||
|
||||
void MinSpinOSO_CG::calc_search_direction(int iter)
|
||||
{
|
||||
int nlocal = atom->nlocal;
|
||||
|
|
@ -286,45 +308,42 @@ void MinSpinOSO_CG::calc_search_direction(int iter)
|
|||
|
||||
// for some reason on a second iteration g_old = 0
|
||||
// so we make two iterations as steepest descent
|
||||
if (iter <= 2 || iter % 5 == 0){
|
||||
// steepest descent direction
|
||||
|
||||
if (iter <= 2 || iter % 5 == 0){ // steepest descent direction
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
for (int j = 0; j < 3; j++){
|
||||
p[3 * i + j] = -g[3 * i + j];
|
||||
g_old[3 * i + j] = g[3 * i + j];
|
||||
}
|
||||
}
|
||||
} else{
|
||||
// conjugate direction
|
||||
} else { // conjugate direction
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
for (int j = 0; j < 3; j++){
|
||||
g2old += g_old[3 * i + j] * g_old[3 * i + j];
|
||||
g2 += g[3 * i + j] * g[3 * i + j];
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
// now we need to collect/broadcast beta on this replica
|
||||
// different replica can have different beta for now.
|
||||
// need to check what is beta for GNEB
|
||||
|
||||
MPI_Allreduce(&g2, &g2_global, 1, MPI_DOUBLE, MPI_SUM, world);
|
||||
MPI_Allreduce(&g2old, &g2old_global, 1, MPI_DOUBLE, MPI_SUM, world);
|
||||
|
||||
beta = g2_global / g2old_global;
|
||||
|
||||
// calculate conjugate direction
|
||||
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
for (int j = 0; j < 3; j++){
|
||||
p[3 * i + j] = beta * p[3 * i + j] - g[3 * i + j];
|
||||
g_old[3 * i + j] = g[3 * i + j];
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
rotation of spins along the search direction
|
||||
---------------------------------------------------------------------- */
|
||||
|
|
@ -342,13 +361,14 @@ void MinSpinOSO_CG::advance_spins()
|
|||
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
rodrigues_rotation(p + 3 * i, rot_mat);
|
||||
|
||||
// rotate spins
|
||||
|
||||
vm3(rot_mat, sp[i], s_new);
|
||||
sp[i][0] = s_new[0];
|
||||
sp[i][1] = s_new[1];
|
||||
sp[i][2] = s_new[2];
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
|
|
@ -384,30 +404,28 @@ double MinSpinOSO_CG::fmnorm_sqr()
|
|||
return norm2_sqr;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
calculate 3x3 matrix exponential using Rodrigues' formula
|
||||
(R. Murray, Z. Li, and S. Shankar Sastry,
|
||||
A Mathematical Introduction to
|
||||
Robotic Manipulation (1994), p. 28 and 30).
|
||||
|
||||
void rodrigues_rotation(const double *upp_tr, double *out){
|
||||
|
||||
/***
|
||||
* calculate 3x3 matrix exponential using Rodrigues' formula
|
||||
* (R. Murray, Z. Li, and S. Shankar Sastry,
|
||||
* A Mathematical Introduction to
|
||||
* Robotic Manipulation (1994), p. 28 and 30).
|
||||
*
|
||||
* upp_tr - vector x, y, z so that one calculate
|
||||
* U = exp(A) with A= [[0, x, y],
|
||||
* [-x, 0, z],
|
||||
* [-y, -z, 0]]
|
||||
***/
|
||||
upp_tr - vector x, y, z so that one calculate
|
||||
U = exp(A) with A= [[0, x, y],
|
||||
[-x, 0, z],
|
||||
[-y, -z, 0]]
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void MinSpinOSO_CG::rodrigues_rotation(const double *upp_tr, double *out)
|
||||
{
|
||||
|
||||
if (fabs(upp_tr[0]) < 1.0e-40 &&
|
||||
fabs(upp_tr[1]) < 1.0e-40 &&
|
||||
fabs(upp_tr[2]) < 1.0e-40){
|
||||
|
||||
// if upp_tr is zero, return unity matrix
|
||||
int k;
|
||||
int m;
|
||||
for(k = 0; k < 3; k++){
|
||||
for(m = 0; m < 3; m++){
|
||||
for(int k = 0; k < 3; k++){
|
||||
for(int m = 0; m < 3; m++){
|
||||
if (m == k) out[3 * k + m] = 1.0;
|
||||
else out[3 * k + m] = 0.0;
|
||||
}
|
||||
|
|
@ -427,11 +445,13 @@ void rodrigues_rotation(const double *upp_tr, double *out){
|
|||
double z = upp_tr[2]/theta;
|
||||
|
||||
// diagonal elements of U
|
||||
|
||||
out[0] = A + z * z * D;
|
||||
out[4] = A + y * y * D;
|
||||
out[8] = A + x * x * D;
|
||||
|
||||
// off diagonal of U
|
||||
|
||||
double s1 = -y * z *D;
|
||||
double s2 = x * z * D;
|
||||
double s3 = -x * y * D;
|
||||
|
|
@ -449,21 +469,17 @@ void rodrigues_rotation(const double *upp_tr, double *out){
|
|||
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
out = vector^T x m,
|
||||
m -- 3x3 matrix , v -- 3-d vector
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void vm3(const double *m, const double *v, double *out){
|
||||
/***
|
||||
* out = vector^T x m,
|
||||
* m -- 3x3 matrix , v -- 3-d vector
|
||||
***/
|
||||
|
||||
int i;
|
||||
int j;
|
||||
|
||||
for(i = 0; i < 3; i++){
|
||||
void MinSpinOSO_CG::vm3(const double *m, const double *v, double *out)
|
||||
{
|
||||
for(int i = 0; i < 3; i++){
|
||||
out[i] *= 0.0;
|
||||
for(j = 0; j < 3; j++){
|
||||
for(int j = 0; j < 3; j++){
|
||||
out[i] += *(m + 3 * j + i) * v[j];
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -13,7 +13,7 @@
|
|||
|
||||
#ifdef MINIMIZE_CLASS
|
||||
|
||||
MinimizeStyle(spin_oso_cg, MinSpinOSO_CG)
|
||||
MinimizeStyle(spin/oso_cg, MinSpinOSO_CG)
|
||||
|
||||
#else
|
||||
|
||||
|
|
@ -27,8 +27,8 @@ namespace LAMMPS_NS {
|
|||
class MinSpinOSO_CG : public Min {
|
||||
|
||||
public:
|
||||
MinSpinOSO_CG(class LAMMPS *); //?
|
||||
~MinSpinOSO_CG() {} //?
|
||||
MinSpinOSO_CG(class LAMMPS *);
|
||||
~MinSpinOSO_CG() {}
|
||||
void init();
|
||||
void setup_style();
|
||||
int modify_param(int, char **);
|
||||
|
|
@ -56,6 +56,9 @@ private:
|
|||
double *g; // gradient vector
|
||||
double *p; // search direction vector
|
||||
|
||||
void vm3(const double *m, const double *v, double *out);
|
||||
void rodrigues_rotation(const double *upp_tr, double *out);
|
||||
|
||||
bigint last_negative;
|
||||
};
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue