forked from lijiext/lammps
add .cpp and .h to root src
This commit is contained in:
Ulf R. Pedersen
parent
75b3f34a58
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348c4eb7f3
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/*
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fix_rhok.cpp
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A fix to add harmonic potential that bias |rho(k)|.
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The usage is as follows:
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fix [name] [groupID] rhoK [nx] [ny] [nz] [kappa = spring constant] [rhoK0]
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where k_i = (2 pi / L_i) * n_i
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Written by Ulf Pedersen and Patrick Varilly, 4 Feb 2010
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Tweaked for LAMMPS 15 Jan 2010 version by Ulf Pedersen, 19 Aug 2010
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Tweaked again March 4th 2012 by Ulf R. Pedersen, and
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September 2017 by Ulf R. Pedersen.
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*/
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#include "fix_rhok.h"
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#include "error.h"
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#include "update.h"
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#include "respa.h"
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#include "atom.h"
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#include "domain.h"
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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 <assert.h>
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#include <math.h>
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using namespace LAMMPS_NS;
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using namespace FixConst;
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// Constructor: all the parameters to this fix specified in
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// the LAMMPS input get passed in
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FixRhok::FixRhok( LAMMPS* inLMP, int inArgc, char** inArgv )
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: Fix( inLMP, inArgc, inArgv )
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{
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// Check arguments
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if( inArgc != 8 )
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error->all(FLERR,"Illegal fix rhoKUmbrella command" );
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// Set up fix flags
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scalar_flag = 1; // have compute_scalar
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vector_flag = 1; // have compute_vector...
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size_vector = 3; // ...with this many components
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global_freq = 1; // whose value can be computed at every timestep
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//scalar_vector_freq = 1; // OLD lammps: whose value can be computed at every timestep
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thermo_energy = 1; // this fix changes system's potential energy
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extscalar = 0; // but the deltaPE might not scale with # of atoms
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extvector = 0; // neither do the components of the vector
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// Parse fix options
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int n[3];
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n[0] = atoi( inArgv[3] );
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n[1] = atoi( inArgv[4] );
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n[2] = atoi( inArgv[5] );
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mK[0] = n[0]*(2*M_PI / (domain->boxhi[0] - domain->boxlo[0]));
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mK[1] = n[1]*(2*M_PI / (domain->boxhi[1] - domain->boxlo[1]));
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mK[2] = n[2]*(2*M_PI / (domain->boxhi[2] - domain->boxlo[2]));
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mKappa = atof( inArgv[6] );
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mRhoK0 = atof( inArgv[7] );
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}
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FixRhok::~FixRhok()
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{
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}
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// Methods that this fix implements
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// --------------------------------
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// Tells LAMMPS where this fix should act
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int
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FixRhok::setmask()
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{
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int mask = 0;
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// This fix modifies forces...
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mask |= POST_FORCE;
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mask |= POST_FORCE_RESPA;
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mask |= MIN_POST_FORCE;
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// ...and potential energies
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mask |= THERMO_ENERGY;
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return mask;
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}
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/*int FixRhok::setmask()
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{
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int mask = 0;
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mask |= POST_FORCE;
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mask |= POST_FORCE_RESPA;
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mask |= MIN_POST_FORCE;
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return mask;
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}*/
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// Initializes the fix at the beginning of a run
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void
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FixRhok::init()
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{
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// RESPA boilerplate
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if( strcmp( update->integrate_style, "respa" ) == 0 )
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mNLevelsRESPA = ((Respa *) update->integrate)->nlevels;
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// Count the number of affected particles
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int nThisLocal = 0;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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for( int i = 0; i < nlocal; i++ ) { // Iterate through all atoms on this CPU
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if( mask[i] & groupbit ) { // ...only those affected by this fix
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nThisLocal++;
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}
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}
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MPI_Allreduce( &nThisLocal, &mNThis,
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1, MPI_INT, MPI_SUM, world );
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mSqrtNThis = sqrt( mNThis );
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}
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// Initial application of the fix to a system (when doing MD)
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void
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FixRhok::setup( int inVFlag )
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{
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if( strcmp( update->integrate_style, "verlet" ) == 0 )
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post_force( inVFlag );
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else
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{
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((Respa *) update->integrate)->copy_flevel_f( mNLevelsRESPA - 1 );
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post_force_respa( inVFlag, mNLevelsRESPA - 1,0 );
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((Respa *) update->integrate)->copy_f_flevel( mNLevelsRESPA - 1 );
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}
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}
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// Initial application of the fix to a system (when doing minimization)
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void
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FixRhok::min_setup( int inVFlag )
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{
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post_force( inVFlag );
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}
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// Modify the forces calculated in the main force loop of ordinary MD
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void
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FixRhok::post_force( int inVFlag )
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{
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double **x = atom->x;
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double **f = atom->f;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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// Loop over locally-owned atoms affected by this fix and calculate the
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// partial rhoK's
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mRhoKLocal[0] = 0.0;
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mRhoKLocal[1] = 0.0;
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for( int i = 0; i < nlocal; i++ ) { // Iterate through all atoms on this CPU
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if( mask[i] & groupbit ) { // ...only those affected by this fix
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// rho_k = sum_i exp( - i k.r_i )
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mRhoKLocal[0] += cos( mK[0]*x[i][0] + mK[1]*x[i][1] + mK[2]*x[i][2] );
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mRhoKLocal[1] -= sin( mK[0]*x[i][0] + mK[1]*x[i][1] + mK[2]*x[i][2] );
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}
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}
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// Now calculate mRhoKGlobal
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MPI_Allreduce( mRhoKLocal, mRhoKGlobal,
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2, MPI_DOUBLE, MPI_SUM, world );
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// Info: < \sum_{i,j} e^{-ik.(r_i - r_j)} > ~ N, so
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// we define rho_k as (1 / sqrt(N)) \sum_i e^{-i k.r_i}, so that
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// <rho_k^2> is intensive.
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mRhoKGlobal[0] /= mSqrtNThis;
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mRhoKGlobal[1] /= mSqrtNThis;
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// We'll need magnitude of rho_k
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double rhoK = sqrt( mRhoKGlobal[0]*mRhoKGlobal[0]
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+ mRhoKGlobal[1]*mRhoKGlobal[1] );
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for( int i = 0; i < nlocal; i++ ) { // Iterate through all atoms on this CPU
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if( mask[i] & groupbit ) { // ...only those affected by this fix
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// Calculate forces
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// U = kappa/2 ( |rho_k| - rho_k^0 )^2
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// f_i = -grad_i U = -kappa ( |rho_k| - rho_k^0 ) grad_i |rho_k|
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// grad_i |rho_k| = Re( rho_k* (-i k e^{-i k . r_i} / sqrt(N)) ) / |rho_k|
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//
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// In terms of real and imag parts of rho_k,
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//
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// Re( rho_k* (-i k e^{-i k . r_i}) ) =
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// (- Re[rho_k] * sin( k . r_i ) - Im[rho_k] * cos( k . r_i )) * k
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double sinKRi = sin( mK[0]*x[i][0] + mK[1]*x[i][1] + mK[2]*x[i][2] );
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double cosKRi = cos( mK[0]*x[i][0] + mK[1]*x[i][1] + mK[2]*x[i][2] );
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double prefactor = mKappa * ( rhoK - mRhoK0 ) / rhoK
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* (-mRhoKGlobal[0]*sinKRi - mRhoKGlobal[1]*cosKRi) / mSqrtNThis;
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f[i][0] -= prefactor * mK[0];
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f[i][1] -= prefactor * mK[1];
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f[i][2] -= prefactor * mK[2];
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}
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}
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}
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// Forces in RESPA loop
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void
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FixRhok::post_force_respa( int inVFlag, int inILevel, int inILoop )
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{
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if( inILevel == mNLevelsRESPA - 1 )
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post_force( inVFlag );
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}
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// Forces in minimization loop
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void
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FixRhok::min_post_force( int inVFlag )
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{
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post_force( inVFlag );
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}
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// Compute the change in the potential energy induced by this fix
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double
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FixRhok::compute_scalar()
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{
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double rhoK = sqrt( mRhoKGlobal[0]*mRhoKGlobal[0]
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+ mRhoKGlobal[1]*mRhoKGlobal[1] );
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return 0.5 * mKappa * (rhoK - mRhoK0) * (rhoK - mRhoK0);
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}
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// Compute the ith component of the vector
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double
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FixRhok::compute_vector( int inI )
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{
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if( inI == 0 )
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return mRhoKGlobal[0]; // Real part
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else if( inI == 1 )
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return mRhoKGlobal[1]; // Imagniary part
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else if( inI == 2 )
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return sqrt( mRhoKGlobal[0]*mRhoKGlobal[0]
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+ mRhoKGlobal[1]*mRhoKGlobal[1] );
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else
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return 12345.0;
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}
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@ -0,0 +1,81 @@
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/*
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fix_rhok.h
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A fix to do umbrella sampling on rho(k).
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The usage is as follows:
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fix [name] [groupID] rhoKUmbrella [kx] [ky] [kz] [kappa = spring constant] [rhoK0]
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where k_i = (2 pi / L_i) * n_i
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Written by Ulf Pedersen and Patrick Varilly, 4 Feb 2010
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Tweaked for LAMMPS 15 Jan 2010 version by Ulf Pedersen, 19 Aug 2010
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*/
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#ifdef FIX_CLASS
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FixStyle(rhok,FixRhok)
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#else
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#ifndef __FIX_RHOK__
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#define __FIX_RHOK__
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#include "fix.h"
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namespace LAMMPS_NS {
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class FixRhok : public Fix
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{
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public:
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// Constructor: all the parameters to this fix specified in
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// the LAMMPS input get passed in
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FixRhok( LAMMPS* inLMP, int inArgc, char** inArgv );
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virtual ~FixRhok();
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// Methods that this fix implements
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// --------------------------------
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// Tells LAMMPS where this fix should act
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int setmask();
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// Initializes the fix at the beginning of a run
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void init();
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// Initial application of the fix to a system (when doing MD / minimization)
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void setup( int inVFlag );
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void min_setup( int inVFlag );
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// Modify the forces calculated in the main force loop, either when
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// doing usual MD, RESPA MD or minimization
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void post_force( int inVFlag );
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void post_force_respa( int inVFlag, int inILevel, int inILoop );
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void min_post_force( int inVFlag );
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// Compute the change in the potential energy induced by this fix
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double compute_scalar();
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// Compute the ith component of the vector associated with this fix
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double compute_vector( int inI );
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private:
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// RESPA boilerplate
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int mNLevelsRESPA;
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// Defining parameters for this umbrella
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double mK[3], mKappa, mRhoK0;
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// Number of particles affected by the fix
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int mNThis;
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double mSqrtNThis;
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// Real and imaginary parts of rho_k := sum_i exp( - i k . r_i )
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double mRhoKLocal[2], mRhoKGlobal[2];
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};
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} // namespace LAMMPS_NS
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#endif // __FIX_RHOK__
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#endif // FIX_CLASS
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