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Commit JT 042418 

- adding the README
- some corrects pair_spin*.cpp/h
This commit is contained in:
julient31 2018-04-24 16:36:30 -06:00
parent 1b8669c620
commit 392816a807
19 changed files with 107 additions and 110 deletions
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5
examples/SPIN/cobalt_fcc/exchange_fit_fcc_co/exchange_fcc_cobalt.dat Normal file
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@ -0,0 +1,5 @@
2.503 0.01476
3.54 0.001497
4.33 0.001578
5.01 -0.001224
5.597 0.000354

32
examples/SPIN/cobalt_fcc/exchange_fit_fcc_co/exchange_fit.py Normal file
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@ -0,0 +1,32 @@
#Program fitting the exchange interaction
#Model curve: Bethe-Slater function
import numpy as np, pylab, tkinter
import matplotlib.pyplot as plt
from scipy.optimize import curve_fit
from decimal import *
print("Loop begin")
#Definition of the Bethe-Slater function
def func(x,a,b,c):
return 4*a*((x/c)**2)*(1-b*(x/c)**2)*np.exp(-(x/c)**2)
#Exchange coeff table (data to fit)
rdata, Jdata = np.loadtxt('exchange_fcc_cobalt.dat', usecols=(0,1), unpack=True)
plt.plot(rdata, Jdata, 'b-', label='data')
#Perform the fit
popt, pcov = curve_fit(func, rdata, Jdata, bounds=(0, [500.,5.,5.]))
plt.plot(rdata, func(rdata, *popt), 'r--', label='fit')
#Print the fitted params
print("Parameters: a={:.10} (in meV), b={:.10} (adim), c={:.10} (in Ang)".format(*popt))
#Ploting the result
plt.xlabel('r_ij')
pylab.xlim([0,6.5])
plt.ylabel('J_ij')
plt.legend()
plt.show()
print("Loop end")

2
examples/SPIN/iron/exchange_fit_bcc_iron/exchange_bcc_iron.dat
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@ -1,3 +1,5 @@
2.4824 0.01948336
2.8665 0.01109
4.0538 -0.0002176
4.753 -0.001714
4.965 -0.001986

10
examples/SPIN/nickel/exchange_fit_fcc_ni/exchange_fcc_ni.dat
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@ -1,5 +1,5 @@
2.495 8.3
3.524 -3.99
4.31 0.998
4.99 -0.955
5.56 0.213
2.492 0.0028027
3.524 0.0000816
4.316 0.0003537
4.984 0.0001632
5.572 0.0000408

5
examples/SPIN/nickel/exchange_fit_fcc_ni/exchange_fcc_ni2.dat Normal file
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@ -0,0 +1,5 @@
2.495 8.3
3.524 -3.99
4.31 0.998
4.99 -0.955
5.56 0.213

5
examples/SPIN/nickel/exchange_fit_fcc_ni/exchange_fit.py
View File

@ -16,7 +16,7 @@ rdata, Jdata = np.loadtxt('exchange_fcc_ni.dat', usecols=(0,1), unpack=True)
plt.plot(rdata, Jdata, 'b-', label='data')
# perform the fit
popt, pcov = curve_fit(func, rdata, Jdata, bounds=(0, [500.,5.,5.]))
popt, pcov = curve_fit(func, rdata, Jdata, bounds=([0.0,-1.0,0.0], [100.,5.,5.]))
plt.plot(rdata, func(rdata, *popt), 'r--', label='fit')
# print the fitted parameters
@ -24,7 +24,8 @@ print("Parameters: a={:.10} (in meV), b={:.10} (adim), c={:.10} (in Ang)".format
# ploting the result
plt.xlabel('r_ij')
pylab.xlim([0,6.5])
pylab.xlim([0.0,6.5])
#pylab.ylim([-2.0,10.0])
plt.ylabel('J_ij')
plt.legend()
plt.show()

25
src/SPIN/README Normal file
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@ -0,0 +1,25 @@
The SPIN package enables coupled spin dynamics and molecular
dynamics simulations.
The package provides the following features:
* defining a classical magnetic atomic spin associated to each magnetic
atom in the system
* integrating the equations of motion for the coupled spin-lattice system
* implementing magnetic pair interactions and magnetic forces
* thermostating and applying a transverse damping to the magnetic spins
* computing and outputing magnetic quantities
The different options provided by this package are explained in the
LAMMPS documentation.
Once you have successfully built LAMMPS with this package, you can test
it using one of the input files provided from the examples/SPIN dir:
./lmp_serial < lammps/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp
== Credits and license ==
The person who created this package is Julien Tranchida (jtranch at
sandia.gov). You can contact him if you have questions.

10
src/SPIN/atom_vec_spin.h
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@ -11,16 +11,6 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ------------------------------------------------------------------------
Contributing authors: Julien Tranchida (SNL)
Aidan Thompson (SNL)
Please cite the related publication:
Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018).
Massively parallel symplectic algorithm for coupled magnetic spin dynamics
and molecular dynamics. arXiv preprint arXiv:1801.10233.
------------------------------------------------------------------------- */
#ifdef ATOM_CLASS
AtomStyle(spin,AtomVecSpin)

10
src/SPIN/compute_spin.h
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@ -11,16 +11,6 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ------------------------------------------------------------------------
Contributing authors: Julien Tranchida (SNL)
Aidan Thompson (SNL)
Please cite the related publication:
Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018).
Massively parallel symplectic algorithm for coupled magnetic spin dynamics
and molecular dynamics. arXiv preprint arXiv:1801.10233.
------------------------------------------------------------------------- */
#ifdef COMPUTE_CLASS
ComputeStyle(compute/spin,ComputeSpin)

10
src/SPIN/fix_langevin_spin.h
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@ -11,16 +11,6 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ------------------------------------------------------------------------
Contributing authors: Julien Tranchida (SNL)
Aidan Thompson (SNL)
Please cite the related publication:
Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018).
Massively parallel symplectic algorithm for coupled magnetic spin dynamics
and molecular dynamics. arXiv preprint arXiv:1801.10233.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(langevin/spin,FixLangevinSpin)

14
src/SPIN/fix_nve_spin.cpp
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@ -27,6 +27,7 @@
#include "atom.h"
#include "atom_vec.h"
#include "citeme.h"
#include "error.h"
#include "fix_precession_spin.h"
#include "fix_nve_spin.h"
@ -50,6 +51,16 @@ using namespace FixConst;
using namespace MathConst;
using namespace MathExtra;
static const char cite_fix_nve_spin[] =
"fix nve/spin command:\n\n"
"@article{tranchida2018massively,\n"
"title={Massively parallel symplectic algorithm for coupled magnetic spin "
"dynamics and molecular dynamics},\n"
"author={Tranchida, J and Plimpton, SJ and Thibaudeau, P and Thompson, AP},\n"
"journal={arXiv preprint arXiv:1801.10233},\n"
"year={2018}\n"
"}\n\n";
enum{NONE};
/* ---------------------------------------------------------------------- */
@ -60,7 +71,8 @@ FixNVESpin::FixNVESpin(LAMMPS *lmp, int narg, char **arg) :
backward_stacks(NULL), forward_stacks(NULL),
pair(NULL), spin_pairs(NULL)
{
if (lmp->citeme) lmp->citeme->add(cite_fix_nve_spin);
if (narg < 4) error->all(FLERR,"Illegal fix/NVE/spin command");
time_integrate = 1;

10
src/SPIN/fix_nve_spin.h
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@ -11,16 +11,6 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ------------------------------------------------------------------------
Contributing authors: Julien Tranchida (SNL)
Aidan Thompson (SNL)
Please cite the related publication:
Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018).
Massively parallel symplectic algorithm for coupled magnetic spin dynamics
and molecular dynamics. arXiv preprint arXiv:1801.10233.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(nve/spin,FixNVESpin)

10
src/SPIN/fix_precession_spin.h
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@ -11,16 +11,6 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ------------------------------------------------------------------------
Contributing authors: Julien Tranchida (SNL)
Aidan Thompson (SNL)
Please cite the related publication:
Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018).
Massively parallel symplectic algorithm for coupled magnetic spin dynamics
and molecular dynamics. arXiv preprint arXiv:1801.10233.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(precession/spin,FixPrecessionSpin)

4
src/SPIN/pair_spin.h
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@ -11,8 +11,12 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
PairStyle(pair/spin,PairSpin)
#else
#ifndef LMP_PAIR_SPIN_H
#define LMP_PAIR_SPIN_H

25
src/SPIN/pair_spin_dmi.cpp
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@ -101,7 +101,6 @@ void PairSpinDmi::settings(int narg, char **arg)
void PairSpinDmi::coeff(int narg, char **arg)
{
// const double hbar = force->hplanck/MY_2PI;
if (!allocated) allocate();
@ -130,15 +129,16 @@ void PairSpinDmi::coeff(int narg, char **arg)
for (int j = MAX(jlo,i); j <= jhi; j++) {
cut_spin_dmi[i][j] = rij;
DM[i][j] = dm;
v_dmx[i][j] = dmx;
v_dmy[i][j] = dmy;
v_dmz[i][j] = dmz;
v_dmx[i][j] = dmx * dm;
v_dmy[i][j] = dmy * dm;
v_dmz[i][j] = dmz * dm;
setflag[i][j] = 1;
count++;
}
}
if (count == 0)
error->all(FLERR,"Incorrect args in pair_style command");
}
/* ----------------------------------------------------------------------
@ -351,7 +351,6 @@ void PairSpinDmi::compute_single_pair(int ii, double fmi[3])
}
/* ----------------------------------------------------------------------
compute the dmi interaction between spin i and spin j
------------------------------------------------------------------------- */
@ -368,13 +367,16 @@ void PairSpinDmi::compute_dmi(int i, int j, double rsq, double fmi[3], double sp
if (rsq <= local_cut2) {
double dmix, dmiy, dmiz;
dmix = DM[itype][jtype] * v_dmx[itype][jtype];
dmiy = DM[itype][jtype] * v_dmy[itype][jtype];
dmiz = DM[itype][jtype] * v_dmz[itype][jtype];
//dmix = DM[itype][jtype] * v_dmx[itype][jtype];
//dmiy = DM[itype][jtype] * v_dmy[itype][jtype];
//dmiz = DM[itype][jtype] * v_dmz[itype][jtype];
dmix = v_dmx[itype][jtype];
dmiy = v_dmy[itype][jtype];
dmiz = v_dmz[itype][jtype];
fmi[0] -= (spj[1]*dmiz - spj[2]*dmiy);
fmi[1] -= (spj[2]*dmix - spj[0]*dmiz);
fmi[2] -= (spj[0]*dmiy - spj[1]*dmix);
fmi[0] += (spj[1]*dmiz - spj[2]*dmiy);
fmi[1] += (spj[2]*dmix - spj[0]*dmiz);
fmi[2] += (spj[0]*dmiy - spj[1]*dmix);
}
}
@ -390,7 +392,6 @@ void PairSpinDmi::compute_dmi_mech(int i, int j, double fi[3], double spi[3], do
fi[2] += 0.0;
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */

10
src/SPIN/pair_spin_dmi.h
View File

@ -11,16 +11,6 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ------------------------------------------------------------------------
Contributing authors: Julien Tranchida (SNL)
Aidan Thompson (SNL)
Please cite the related publication:
Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018).
Massively parallel symplectic algorithm for coupled magnetic spin dynamics
and molecular dynamics. arXiv preprint arXiv:1801.10233.
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
PairStyle(spin/dmi,PairSpinDmi)

10
src/SPIN/pair_spin_exchange.h
View File

@ -11,16 +11,6 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ------------------------------------------------------------------------
Contributing authors: Julien Tranchida (SNL)
Aidan Thompson (SNL)
Please cite the related publication:
Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018).
Massively parallel symplectic algorithm for coupled magnetic spin dynamics
and molecular dynamics. arXiv preprint arXiv:1801.10233.
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
PairStyle(spin/exchange,PairSpinExchange)

10
src/SPIN/pair_spin_me.h
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@ -11,16 +11,6 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ------------------------------------------------------------------------
Contributing authors: Julien Tranchida (SNL)
Aidan Thompson (SNL)
Please cite the related publication:
Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018).
Massively parallel symplectic algorithm for coupled magnetic spin dynamics
and molecular dynamics. arXiv preprint arXiv:1801.10233.
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
PairStyle(spin/me,PairSpinMe)

10
src/SPIN/pair_spin_neel.h
View File

@ -11,16 +11,6 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ------------------------------------------------------------------------
Contributing authors: Julien Tranchida (SNL)
Aidan Thompson (SNL)
Please cite the related publication:
Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018).
Massively parallel symplectic algorithm for coupled magnetic spin dynamics
and molecular dynamics. arXiv preprint arXiv:1801.10233.
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
PairStyle(spin/neel,PairSpinNeel)