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lammps/src/USER-MISC/fix_rhok.cpp
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fix_rhok.cpp
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/*
fix_rhok.cpp
A fix to add harmonic potential that bias |rho(k)|.
The usage is as follows:
fix [name] [groupID] rhok [nx] [ny] [nz] [K] [a]
where k_i = (2 pi / L_i) * n_i
Written by Ulf Pedersen and Patrick Varilly, 4 Feb 2010
Tweaked for LAMMPS 15 Jan 2010 version by Ulf Pedersen, 19 Aug 2010
Tweaked again March 4th 2012 by Ulf R. Pedersen, and
September 2017 by Ulf R. Pedersen.
*/
#include "fix_rhok.h"
#include "error.h"
#include "update.h"
#include "respa.h"
#include "atom.h"
#include "domain.h"
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <assert.h>
#include <math.h>
using namespace LAMMPS_NS;
using namespace FixConst;
// Constructor: all the parameters to this fix specified in
// the LAMMPS input get passed in
FixRhok::FixRhok( LAMMPS* inLMP, int inArgc, char** inArgv )
: Fix( inLMP, inArgc, inArgv )
{
// Check arguments
if( inArgc != 8 )
error->all(FLERR,"Illegal fix rhoKUmbrella command" );
// Set up fix flags
scalar_flag = 1; // have compute_scalar
vector_flag = 1; // have compute_vector...
size_vector = 3; // ...with this many components
global_freq = 1; // whose value can be computed at every timestep
//scalar_vector_freq = 1; // OLD lammps: whose value can be computed at every timestep
thermo_energy = 1; // this fix changes system's potential energy
extscalar = 0; // but the deltaPE might not scale with # of atoms
extvector = 0; // neither do the components of the vector
// Parse fix options
int n[3];
n[0] = atoi( inArgv[3] );
n[1] = atoi( inArgv[4] );
n[2] = atoi( inArgv[5] );
mK[0] = n[0]*(2*M_PI / (domain->boxhi[0] - domain->boxlo[0]));
mK[1] = n[1]*(2*M_PI / (domain->boxhi[1] - domain->boxlo[1]));
mK[2] = n[2]*(2*M_PI / (domain->boxhi[2] - domain->boxlo[2]));
mKappa = atof( inArgv[6] );
mRhoK0 = atof( inArgv[7] );
}
FixRhok::~FixRhok()
{
}
// Methods that this fix implements
// --------------------------------
// Tells LAMMPS where this fix should act
int
FixRhok::setmask()
{
int mask = 0;
// This fix modifies forces...
mask |= POST_FORCE;
mask |= POST_FORCE_RESPA;
mask |= MIN_POST_FORCE;
// ...and potential energies
mask |= THERMO_ENERGY;
return mask;
}
/*int FixRhok::setmask()
{
int mask = 0;
mask |= POST_FORCE;
mask |= POST_FORCE_RESPA;
mask |= MIN_POST_FORCE;
return mask;
}*/
// Initializes the fix at the beginning of a run
void
FixRhok::init()
{
// RESPA boilerplate
if( strcmp( update->integrate_style, "respa" ) == 0 )
mNLevelsRESPA = ((Respa *) update->integrate)->nlevels;
// Count the number of affected particles
int nThisLocal = 0;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for( int i = 0; i < nlocal; i++ ) { // Iterate through all atoms on this CPU
if( mask[i] & groupbit ) { // ...only those affected by this fix
nThisLocal++;
}
}
MPI_Allreduce( &nThisLocal, &mNThis,
1, MPI_INT, MPI_SUM, world );
mSqrtNThis = sqrt( mNThis );
}
// Initial application of the fix to a system (when doing MD)
void
FixRhok::setup( int inVFlag )
{
if( strcmp( update->integrate_style, "verlet" ) == 0 )
post_force( inVFlag );
else
{
((Respa *) update->integrate)->copy_flevel_f( mNLevelsRESPA - 1 );
post_force_respa( inVFlag, mNLevelsRESPA - 1,0 );
((Respa *) update->integrate)->copy_f_flevel( mNLevelsRESPA - 1 );
}
}
// Initial application of the fix to a system (when doing minimization)
void
FixRhok::min_setup( int inVFlag )
{
post_force( inVFlag );
}
// Modify the forces calculated in the main force loop of ordinary MD
void
FixRhok::post_force( int inVFlag )
{
double **x = atom->x;
double **f = atom->f;
int *mask = atom->mask;
int nlocal = atom->nlocal;
// Loop over locally-owned atoms affected by this fix and calculate the
// partial rhoK's
mRhoKLocal[0] = 0.0;
mRhoKLocal[1] = 0.0;
for( int i = 0; i < nlocal; i++ ) { // Iterate through all atoms on this CPU
if( mask[i] & groupbit ) { // ...only those affected by this fix
// rho_k = sum_i exp( - i k.r_i )
mRhoKLocal[0] += cos( mK[0]*x[i][0] + mK[1]*x[i][1] + mK[2]*x[i][2] );
mRhoKLocal[1] -= sin( mK[0]*x[i][0] + mK[1]*x[i][1] + mK[2]*x[i][2] );
}
}
// Now calculate mRhoKGlobal
MPI_Allreduce( mRhoKLocal, mRhoKGlobal,
2, MPI_DOUBLE, MPI_SUM, world );
// Info: < \sum_{i,j} e^{-ik.(r_i - r_j)} > ~ N, so
// we define rho_k as (1 / sqrt(N)) \sum_i e^{-i k.r_i}, so that
// <rho_k^2> is intensive.
mRhoKGlobal[0] /= mSqrtNThis;
mRhoKGlobal[1] /= mSqrtNThis;
// We'll need magnitude of rho_k
double rhoK = sqrt( mRhoKGlobal[0]*mRhoKGlobal[0]
+ mRhoKGlobal[1]*mRhoKGlobal[1] );
for( int i = 0; i < nlocal; i++ ) { // Iterate through all atoms on this CPU
if( mask[i] & groupbit ) { // ...only those affected by this fix
// Calculate forces
// U = kappa/2 ( |rho_k| - rho_k^0 )^2
// f_i = -grad_i U = -kappa ( |rho_k| - rho_k^0 ) grad_i |rho_k|
// grad_i |rho_k| = Re( rho_k* (-i k e^{-i k . r_i} / sqrt(N)) ) / |rho_k|
//
// In terms of real and imag parts of rho_k,
//
// Re( rho_k* (-i k e^{-i k . r_i}) ) =
// (- Re[rho_k] * sin( k . r_i ) - Im[rho_k] * cos( k . r_i )) * k
double sinKRi = sin( mK[0]*x[i][0] + mK[1]*x[i][1] + mK[2]*x[i][2] );
double cosKRi = cos( mK[0]*x[i][0] + mK[1]*x[i][1] + mK[2]*x[i][2] );
double prefactor = mKappa * ( rhoK - mRhoK0 ) / rhoK
* (-mRhoKGlobal[0]*sinKRi - mRhoKGlobal[1]*cosKRi) / mSqrtNThis;
f[i][0] -= prefactor * mK[0];
f[i][1] -= prefactor * mK[1];
f[i][2] -= prefactor * mK[2];
}
}
}
// Forces in RESPA loop
void
FixRhok::post_force_respa( int inVFlag, int inILevel, int inILoop )
{
if( inILevel == mNLevelsRESPA - 1 )
post_force( inVFlag );
}
// Forces in minimization loop
void
FixRhok::min_post_force( int inVFlag )
{
post_force( inVFlag );
}
// Compute the change in the potential energy induced by this fix
double
FixRhok::compute_scalar()
{
double rhoK = sqrt( mRhoKGlobal[0]*mRhoKGlobal[0]
+ mRhoKGlobal[1]*mRhoKGlobal[1] );
return 0.5 * mKappa * (rhoK - mRhoK0) * (rhoK - mRhoK0);
}
// Compute the ith component of the vector
double
FixRhok::compute_vector( int inI )
{
if( inI == 0 )
return mRhoKGlobal[0]; // Real part
else if( inI == 1 )
return mRhoKGlobal[1]; // Imagniary part
else if( inI == 2 )
return sqrt( mRhoKGlobal[0]*mRhoKGlobal[0]
+ mRhoKGlobal[1]*mRhoKGlobal[1] );
else
return 12345.0;
}
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