From fe8244c1c2320b0af83ce739b6a4b55ebbe39237 Mon Sep 17 00:00:00 2001 From: "Ulf R. Pedersen" Date: Thu, 21 Sep 2017 16:49:46 +0200 Subject: [PATCH] Rename fix --- .../{fix_rhoKUmbrella.cpp => fix_rhok.cpp} | 35 +++++++++---------- .../{fix_rhoKUmbrella.h => fix_rhok.h} | 16 ++++----- 2 files changed, 25 insertions(+), 26 deletions(-) rename src/USER-PINNING/{fix_rhoKUmbrella.cpp => fix_rhok.cpp} (87%) rename src/USER-PINNING/{fix_rhoKUmbrella.h => fix_rhok.h} (85%) diff --git a/src/USER-PINNING/fix_rhoKUmbrella.cpp b/src/USER-PINNING/fix_rhok.cpp similarity index 87% rename from src/USER-PINNING/fix_rhoKUmbrella.cpp rename to src/USER-PINNING/fix_rhok.cpp index e62eecb31c..5cbc85a0d6 100644 --- a/src/USER-PINNING/fix_rhoKUmbrella.cpp +++ b/src/USER-PINNING/fix_rhok.cpp @@ -5,16 +5,17 @@ The usage is as follows: - fix [name] [groupID] rhoKUmbrella [nx] [ny] [nz] [kappa = spring constant] [rhoK0] + 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 Pedersen. + Tweaked again March 4th 2012 by Ulf R. Pedersen, + September 2016 by Ulf R. Pedersen */ -#include "fix_rhoKUmbrella.h" +#include "fix_rhok.h" #include "error.h" #include "update.h" #include "respa.h" @@ -32,7 +33,7 @@ using namespace FixConst; // Constructor: all the parameters to this fix specified in // the LAMMPS input get passed in -FixRhoKUmbrella::FixRhoKUmbrella( LAMMPS* inLMP, int inArgc, char** inArgv ) +FixRhok::FixRhok( LAMMPS* inLMP, int inArgc, char** inArgv ) : Fix( inLMP, inArgc, inArgv ) { // Check arguments @@ -64,7 +65,7 @@ FixRhoKUmbrella::FixRhoKUmbrella( LAMMPS* inLMP, int inArgc, char** inArgv ) mRhoK0 = atof( inArgv[7] ); } -FixRhoKUmbrella::~FixRhoKUmbrella() +FixRhok::~FixRhok() { } @@ -73,7 +74,7 @@ FixRhoKUmbrella::~FixRhoKUmbrella() // Tells LAMMPS where this fix should act int -FixRhoKUmbrella::setmask() +FixRhok::setmask() { int mask = 0; @@ -88,7 +89,7 @@ FixRhoKUmbrella::setmask() return mask; } -/*int FixRhoKUmbrella::setmask() +/*int FixRhok::setmask() { int mask = 0; mask |= POST_FORCE; @@ -100,7 +101,7 @@ FixRhoKUmbrella::setmask() // Initializes the fix at the beginning of a run void -FixRhoKUmbrella::init() +FixRhok::init() { // RESPA boilerplate if( strcmp( update->integrate_style, "respa" ) == 0 ) @@ -122,7 +123,7 @@ FixRhoKUmbrella::init() // Initial application of the fix to a system (when doing MD) void -FixRhoKUmbrella::setup( int inVFlag ) +FixRhok::setup( int inVFlag ) { if( strcmp( update->integrate_style, "verlet" ) == 0 ) post_force( inVFlag ); @@ -136,14 +137,14 @@ FixRhoKUmbrella::setup( int inVFlag ) // Initial application of the fix to a system (when doing minimization) void -FixRhoKUmbrella::min_setup( int inVFlag ) +FixRhok::min_setup( int inVFlag ) { post_force( inVFlag ); } // Modify the forces calculated in the main force loop of ordinary MD void -FixRhoKUmbrella::post_force( int inVFlag ) +FixRhok::post_force( int inVFlag ) { double **x = atom->x; double **f = atom->f; @@ -168,11 +169,9 @@ FixRhoKUmbrella::post_force( int inVFlag ) MPI_Allreduce( mRhoKLocal, mRhoKGlobal, 2, MPI_DOUBLE, MPI_SUM, world ); - // WARNING!!!!! < \sum_{i,j} e^{-ik.(r_i - r_j)} > ~ N, so + // 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 // is intensive. - // - // Don't forget this two years from now when you change the system size!!! mRhoKGlobal[0] /= mSqrtNThis; mRhoKGlobal[1] /= mSqrtNThis; @@ -207,7 +206,7 @@ FixRhoKUmbrella::post_force( int inVFlag ) // Forces in RESPA loop void -FixRhoKUmbrella::post_force_respa( int inVFlag, int inILevel, int inILoop ) +FixRhok::post_force_respa( int inVFlag, int inILevel, int inILoop ) { if( inILevel == mNLevelsRESPA - 1 ) post_force( inVFlag ); @@ -215,14 +214,14 @@ FixRhoKUmbrella::post_force_respa( int inVFlag, int inILevel, int inILoop ) // Forces in minimization loop void -FixRhoKUmbrella::min_post_force( int inVFlag ) +FixRhok::min_post_force( int inVFlag ) { post_force( inVFlag ); } // Compute the change in the potential energy induced by this fix double -FixRhoKUmbrella::compute_scalar() +FixRhok::compute_scalar() { double rhoK = sqrt( mRhoKGlobal[0]*mRhoKGlobal[0] + mRhoKGlobal[1]*mRhoKGlobal[1] ); @@ -232,7 +231,7 @@ FixRhoKUmbrella::compute_scalar() // Compute the ith component of the vector double -FixRhoKUmbrella::compute_vector( int inI ) +FixRhok::compute_vector( int inI ) { if( inI == 0 ) return mRhoKGlobal[0]; // Real part diff --git a/src/USER-PINNING/fix_rhoKUmbrella.h b/src/USER-PINNING/fix_rhok.h similarity index 85% rename from src/USER-PINNING/fix_rhoKUmbrella.h rename to src/USER-PINNING/fix_rhok.h index d549d31d94..3e0625430f 100644 --- a/src/USER-PINNING/fix_rhoKUmbrella.h +++ b/src/USER-PINNING/fix_rhok.h @@ -1,5 +1,5 @@ /* - fix_rhoK_umbrella.h + fix_rhok.h A fix to do umbrella sampling on rho(k). @@ -15,24 +15,24 @@ #ifdef FIX_CLASS -FixStyle(rhoKUmbrella,FixRhoKUmbrella) +FixStyle(rhok,FixRhok) #else -#ifndef __FIX_RHOKUMBRELLA__ -#define __FIX_RHOKUMBRELLA__ +#ifndef __FIX_RHOK__ +#define __FIX_RHOK__ #include "fix.h" namespace LAMMPS_NS { -class FixRhoKUmbrella : public Fix +class FixRhok : public Fix { public: // Constructor: all the parameters to this fix specified in // the LAMMPS input get passed in - FixRhoKUmbrella( LAMMPS* inLMP, int inArgc, char** inArgv ); - virtual ~FixRhoKUmbrella(); + FixRhok( LAMMPS* inLMP, int inArgc, char** inArgv ); + virtual ~FixRhok(); // Methods that this fix implements // -------------------------------- @@ -76,6 +76,6 @@ private: } // namespace LAMMPS_NS -#endif // __FIX_RHOKUMBRELLA__ +#endif // __FIX_RHOK__ #endif // FIX_CLASS