Delete fix_rhok.cpp

/*

 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] [kappa = spring constant] [rhoK0]

 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;

}