Loading src/fix_rhok.cpp 0 → 100644 +245 −0 Original line number Diff line number Diff line /* 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; } src/fix_rhok.h 0 → 100644 +81 −0 Original line number Diff line number Diff line /* fix_rhok.h A fix to do umbrella sampling on rho(k). The usage is as follows: fix [name] [groupID] rhoKUmbrella [kx] [ky] [kz] [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 */ #ifdef FIX_CLASS FixStyle(rhok,FixRhok) #else #ifndef __FIX_RHOK__ #define __FIX_RHOK__ #include "fix.h" namespace LAMMPS_NS { class FixRhok : public Fix { public: // Constructor: all the parameters to this fix specified in // the LAMMPS input get passed in FixRhok( LAMMPS* inLMP, int inArgc, char** inArgv ); virtual ~FixRhok(); // Methods that this fix implements // -------------------------------- // Tells LAMMPS where this fix should act int setmask(); // Initializes the fix at the beginning of a run void init(); // Initial application of the fix to a system (when doing MD / minimization) void setup( int inVFlag ); void min_setup( int inVFlag ); // Modify the forces calculated in the main force loop, either when // doing usual MD, RESPA MD or minimization void post_force( int inVFlag ); void post_force_respa( int inVFlag, int inILevel, int inILoop ); void min_post_force( int inVFlag ); // Compute the change in the potential energy induced by this fix double compute_scalar(); // Compute the ith component of the vector associated with this fix double compute_vector( int inI ); private: // RESPA boilerplate int mNLevelsRESPA; // Defining parameters for this umbrella double mK[3], mKappa, mRhoK0; // Number of particles affected by the fix int mNThis; double mSqrtNThis; // Real and imaginary parts of rho_k := sum_i exp( - i k . r_i ) double mRhoKLocal[2], mRhoKGlobal[2]; }; } // namespace LAMMPS_NS #endif // __FIX_RHOK__ #endif // FIX_CLASS Loading
src/fix_rhok.cpp 0 → 100644 +245 −0 Original line number Diff line number Diff line /* 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; }
src/fix_rhok.h 0 → 100644 +81 −0 Original line number Diff line number Diff line /* fix_rhok.h A fix to do umbrella sampling on rho(k). The usage is as follows: fix [name] [groupID] rhoKUmbrella [kx] [ky] [kz] [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 */ #ifdef FIX_CLASS FixStyle(rhok,FixRhok) #else #ifndef __FIX_RHOK__ #define __FIX_RHOK__ #include "fix.h" namespace LAMMPS_NS { class FixRhok : public Fix { public: // Constructor: all the parameters to this fix specified in // the LAMMPS input get passed in FixRhok( LAMMPS* inLMP, int inArgc, char** inArgv ); virtual ~FixRhok(); // Methods that this fix implements // -------------------------------- // Tells LAMMPS where this fix should act int setmask(); // Initializes the fix at the beginning of a run void init(); // Initial application of the fix to a system (when doing MD / minimization) void setup( int inVFlag ); void min_setup( int inVFlag ); // Modify the forces calculated in the main force loop, either when // doing usual MD, RESPA MD or minimization void post_force( int inVFlag ); void post_force_respa( int inVFlag, int inILevel, int inILoop ); void min_post_force( int inVFlag ); // Compute the change in the potential energy induced by this fix double compute_scalar(); // Compute the ith component of the vector associated with this fix double compute_vector( int inI ); private: // RESPA boilerplate int mNLevelsRESPA; // Defining parameters for this umbrella double mK[3], mKappa, mRhoK0; // Number of particles affected by the fix int mNThis; double mSqrtNThis; // Real and imaginary parts of rho_k := sum_i exp( - i k . r_i ) double mRhoKLocal[2], mRhoKGlobal[2]; }; } // namespace LAMMPS_NS #endif // __FIX_RHOK__ #endif // FIX_CLASS
