diff --git a/src/SPIN/fix_neb_spin.cpp b/src/SPIN/fix_neb_spin.cpp index 714335c885..2a368d5dc9 100644 --- a/src/SPIN/fix_neb_spin.cpp +++ b/src/SPIN/fix_neb_spin.cpp @@ -49,7 +49,7 @@ enum{SINGLE_PROC_DIRECT,SINGLE_PROC_MAP,MULTI_PROC}; /* ---------------------------------------------------------------------- */ -FixNEB_spin::FixNEB_spin(LAMMPS *lmp, int narg, char **arg) : +FixNEBSpin::FixNEBSpin(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), id_pe(NULL), pe(NULL), nlenall(NULL), xprev(NULL), xnext(NULL), fnext(NULL), spprev(NULL), spnext(NULL), fmnext(NULL), springF(NULL), tangent(NULL), xsend(NULL), xrecv(NULL), fsend(NULL), frecv(NULL), spsend(NULL), @@ -144,7 +144,7 @@ FixNEB_spin::FixNEB_spin(LAMMPS *lmp, int narg, char **arg) : /* ---------------------------------------------------------------------- */ -FixNEB_spin::~FixNEB_spin() +FixNEBSpin::~FixNEBSpin() { modify->delete_compute(id_pe); delete [] id_pe; @@ -192,7 +192,7 @@ FixNEB_spin::~FixNEB_spin() /* ---------------------------------------------------------------------- */ -int FixNEB_spin::setmask() +int FixNEBSpin::setmask() { int mask = 0; mask |= MIN_POST_FORCE; @@ -201,7 +201,7 @@ int FixNEB_spin::setmask() /* ---------------------------------------------------------------------- */ -void FixNEB_spin::init() +void FixNEBSpin::init() { int icompute = modify->find_compute(id_pe); if (icompute < 0) @@ -251,7 +251,7 @@ void FixNEB_spin::init() /* ---------------------------------------------------------------------- */ -void FixNEB_spin::min_setup(int vflag) +void FixNEBSpin::min_setup(int vflag) { min_post_force(vflag); @@ -262,7 +262,7 @@ void FixNEB_spin::min_setup(int vflag) /* ---------------------------------------------------------------------- */ -void FixNEB_spin::min_post_force(int /*vflag*/) +void FixNEBSpin::min_post_force(int /*vflag*/) { double vprev,vnext; double delspxp,delspyp,delspzp; @@ -289,15 +289,15 @@ void FixNEB_spin::min_post_force(int /*vflag*/) } if (FreeEndFinal && ireplica == nreplica-1 && (update->ntimestep == 0)) - error->all(FLERR,"NEB_spin Free End option not yet active"); + error->all(FLERR,"NEBSpin Free End option not yet active"); if (ireplica == 0) vIni=veng; if (FreeEndFinalWithRespToEIni) - error->all(FLERR,"NEB_spin Free End option not yet active"); + error->all(FLERR,"NEBSpin Free End option not yet active"); if (FreeEndIni && ireplica == 0 && (update->ntimestep == 0)) - error->all(FLERR,"NEB_spin Free End option not yet active"); + error->all(FLERR,"NEBSpin Free End option not yet active"); // communicate atoms to/from adjacent replicas to fill xprev,xnext @@ -505,7 +505,7 @@ void FixNEB_spin::min_post_force(int /*vflag*/) // no Perpendicular nudging force option active yet if (kspringPerp != 0.0) - error->all(FLERR,"NEB_spin Perpendicular spring force not yet active"); + error->all(FLERR,"NEBSpin Perpendicular spring force not yet active"); } } @@ -569,16 +569,16 @@ void FixNEB_spin::min_post_force(int /*vflag*/) // no Free End options active yet if (FreeEndIni && ireplica == 0) - error->all(FLERR,"NEB_spin Free End option not yet active"); + error->all(FLERR,"NEBSpin Free End option not yet active"); if (FreeEndFinal && ireplica == nreplica -1) - error->all(FLERR,"NEB_spin Free End option not yet active"); + error->all(FLERR,"NEBSpin Free End option not yet active"); if (FreeEndFinalWithRespToEIni&&ireplica == nreplica -1) - error->all(FLERR,"NEB_spin Free End option not yet active"); + error->all(FLERR,"NEBSpin Free End option not yet active"); - // no NEB_spin long range option + // no NEBSpin long range option if (NEBLongRange) - error->all(FLERR,"NEB_spin long range option not yet active"); + error->all(FLERR,"NEBSpin long range option not yet active"); // exit calc. if first or last replica (no gneb force) @@ -604,7 +604,7 @@ void FixNEB_spin::min_post_force(int /*vflag*/) if (ireplica == rclimber) prefactor = -2.0*dot; // for climbing replica else { if (NEBLongRange) { - error->all(FLERR,"Long Range NEB_spin climber option not yet active"); + error->all(FLERR,"Long Range NEBSpin climber option not yet active"); } else if (StandardNEB) { prefactor = -dot + kspring*(nlen-plen); } @@ -645,7 +645,7 @@ void FixNEB_spin::min_post_force(int /*vflag*/) geodesic distance calculation (Vincenty's formula) ------------------------------------------------------------------------- */ -double FixNEB_spin::geodesic_distance(double spi[3], double spj[3]) +double FixNEBSpin::geodesic_distance(double spi[3], double spj[3]) { double dist; double crossx,crossy,crossz; @@ -676,7 +676,7 @@ double FixNEB_spin::geodesic_distance(double spi[3], double spj[3]) replicas 0 and N-1 send but do not receive any atoms ------------------------------------------------------------------------- */ -void FixNEB_spin::inter_replica_comm() +void FixNEBSpin::inter_replica_comm() { int i,m; MPI_Request request; @@ -956,7 +956,7 @@ void FixNEB_spin::inter_replica_comm() reallocate communication arrays if necessary ------------------------------------------------------------------------- */ -void FixNEB_spin::reallocate() +void FixNEBSpin::reallocate() { maxlocal = atom->nmax; diff --git a/src/SPIN/fix_neb_spin.h b/src/SPIN/fix_neb_spin.h index 8e016b2e23..7ac83ddce7 100644 --- a/src/SPIN/fix_neb_spin.h +++ b/src/SPIN/fix_neb_spin.h @@ -13,7 +13,7 @@ #ifdef FIX_CLASS -FixStyle(neb/spin,FixNEB_spin) +FixStyle(neb/spin,FixNEBSpin) #else @@ -24,13 +24,13 @@ FixStyle(neb/spin,FixNEB_spin) namespace LAMMPS_NS { -class FixNEB_spin : public Fix { +class FixNEBSpin : public Fix { public: double veng,plen,nlen,dotpath,dottangrad,gradlen,dotgrad; int rclimber; - FixNEB_spin(class LAMMPS *, int, char **); - ~FixNEB_spin(); + FixNEBSpin(class LAMMPS *, int, char **); + ~FixNEBSpin(); int setmask(); void init(); void min_setup(int); diff --git a/src/SPIN/neb_spin.cpp b/src/SPIN/neb_spin.cpp index 44e67eb014..db8469ed63 100644 --- a/src/SPIN/neb_spin.cpp +++ b/src/SPIN/neb_spin.cpp @@ -76,15 +76,15 @@ static const char cite_neb_spin[] = /* ---------------------------------------------------------------------- */ -NEB_spin::NEB_spin(LAMMPS *lmp) : Pointers(lmp) { +NEBSpin::NEBSpin(LAMMPS *lmp) : Pointers(lmp) { if (lmp->citeme) lmp->citeme->add(cite_neb_spin); } /* ---------------------------------------------------------------------- - internal NEB_spin constructor, called from TAD + internal NEBSpin constructor, called from TAD ------------------------------------------------------------------------- */ -NEB_spin::NEB_spin(LAMMPS *lmp, double etol_in, double ftol_in, int n1steps_in, +NEBSpin::NEBSpin(LAMMPS *lmp, double etol_in, double ftol_in, int n1steps_in, int n2steps_in, int nevery_in, double *buf_init, double *buf_final) : Pointers(lmp) { @@ -155,7 +155,7 @@ NEB_spin::NEB_spin(LAMMPS *lmp, double etol_in, double ftol_in, int n1steps_in, /* ---------------------------------------------------------------------- */ -NEB_spin::~NEB_spin() +NEBSpin::~NEBSpin() { MPI_Comm_free(&roots); memory->destroy(all); @@ -163,15 +163,15 @@ NEB_spin::~NEB_spin() } /* ---------------------------------------------------------------------- - perform NEB_spin on multiple replicas + perform NEBSpin on multiple replicas ------------------------------------------------------------------------- */ -void NEB_spin::command(int narg, char **arg) +void NEBSpin::command(int narg, char **arg) { if (domain->box_exist == 0) - error->all(FLERR,"NEB_spin command before simulation box is defined"); + error->all(FLERR,"NEBSpin command before simulation box is defined"); - if (narg < 6) error->universe_all(FLERR,"Illegal NEB_spin command"); + if (narg < 6) error->universe_all(FLERR,"Illegal NEBSpin command"); etol = force->numeric(FLERR,arg[0]); ttol = force->numeric(FLERR,arg[1]); @@ -181,11 +181,11 @@ void NEB_spin::command(int narg, char **arg) // error checks - if (etol < 0.0) error->all(FLERR,"Illegal NEB_spin command"); - if (ttol < 0.0) error->all(FLERR,"Illegal NEB_spin command"); - if (nevery <= 0) error->universe_all(FLERR,"Illegal NEB_spin command"); + if (etol < 0.0) error->all(FLERR,"Illegal NEBSpin command"); + if (ttol < 0.0) error->all(FLERR,"Illegal NEBSpin command"); + if (nevery <= 0) error->universe_all(FLERR,"Illegal NEBSpin command"); if (n1steps % nevery || n2steps % nevery) - error->universe_all(FLERR,"Illegal NEB_spin command"); + error->universe_all(FLERR,"Illegal NEBSpin command"); // replica info @@ -204,23 +204,23 @@ void NEB_spin::command(int narg, char **arg) // error checks - if (nreplica == 1) error->all(FLERR,"Cannot use NEB_spin with a single replica"); + if (nreplica == 1) error->all(FLERR,"Cannot use NEBSpin with a single replica"); if (atom->map_style == 0) - error->all(FLERR,"Cannot use NEB_spin unless atom map exists"); + error->all(FLERR,"Cannot use NEBSpin unless atom map exists"); // process file-style setting to setup initial configs for all replicas if (strcmp(arg[5],"final") == 0) { - if (narg != 7 && narg !=8) error->universe_all(FLERR,"Illegal NEB_spin command"); + if (narg != 7 && narg !=8) error->universe_all(FLERR,"Illegal NEBSpin command"); infile = arg[6]; readfile(infile,0); } else if (strcmp(arg[5],"each") == 0) { - if (narg != 7 && narg !=8) error->universe_all(FLERR,"Illegal NEB_spin command"); + if (narg != 7 && narg !=8) error->universe_all(FLERR,"Illegal NEBSpin command"); infile = arg[6]; readfile(infile,1); } else if (strcmp(arg[5],"none") == 0) { - if (narg != 6 && narg !=7) error->universe_all(FLERR,"Illegal NEB_spin command"); - } else error->universe_all(FLERR,"Illegal NEB_spin command"); + if (narg != 6 && narg !=7) error->universe_all(FLERR,"Illegal NEBSpin command"); + } else error->universe_all(FLERR,"Illegal NEBSpin command"); verbose=false; if (strcmp(arg[narg-1],"verbose") == 0) verbose=true; @@ -229,10 +229,10 @@ void NEB_spin::command(int narg, char **arg) } /* ---------------------------------------------------------------------- - run NEB_spin on multiple replicas + run NEBSpin on multiple replicas ------------------------------------------------------------------------- */ -void NEB_spin::run() +void NEBSpin::run() { // create MPI communicator for root proc from each world @@ -246,9 +246,9 @@ void NEB_spin::run() int ineb; for (ineb = 0; ineb < modify->nfix; ineb++) if (strcmp(modify->fix[ineb]->style,"neb/spin") == 0) break; - if (ineb == modify->nfix) error->all(FLERR,"NEB_spin requires use of fix neb/spin"); + if (ineb == modify->nfix) error->all(FLERR,"NEBSpin requires use of fix neb/spin"); - fneb = (FixNEB_spin *) modify->fix[ineb]; + fneb = (FixNEBSpin *) modify->fix[ineb]; if (verbose) numall =7; else numall = 4; memory->create(all,nreplica,numall,"neb:all"); @@ -266,24 +266,24 @@ void NEB_spin::run() // check if correct minimizer is setup if (update->minimize->searchflag) - error->all(FLERR,"NEB_spin requires damped dynamics minimizer"); + error->all(FLERR,"NEBSpin requires damped dynamics minimizer"); if (strcmp(update->minimize_style,"spin") != 0) - error->all(FLERR,"NEB_spin requires spin minimizer"); + error->all(FLERR,"NEBSpin requires spin minimizer"); - // setup regular NEB_spin minimization + // setup regular NEBSpin minimization FILE *uscreen = universe->uscreen; FILE *ulogfile = universe->ulogfile; if (me_universe == 0 && uscreen) - fprintf(uscreen,"Setting up regular NEB_spin ...\n"); + fprintf(uscreen,"Setting up regular NEBSpin ...\n"); update->beginstep = update->firststep = update->ntimestep; update->endstep = update->laststep = update->firststep + n1steps; update->nsteps = n1steps; update->max_eval = n1steps; if (update->laststep < 0) - error->all(FLERR,"Too many timesteps for NEB_spin"); + error->all(FLERR,"Too many timesteps for NEBSpin"); update->minimize->setup(); @@ -316,8 +316,8 @@ void NEB_spin::run() } print_status(); - // perform regular NEB_spin for n1steps or until replicas converge - // retrieve PE values from fix NEB_spin and print every nevery iterations + // perform regular NEBSpin for n1steps or until replicas converge + // retrieve PE values from fix NEBSpin and print every nevery iterations // break out of while loop early if converged // damped dynamic min styles insure all replicas converge together @@ -337,7 +337,7 @@ void NEB_spin::run() Finish finish(lmp); finish.end(1); - // switch fix NEB_spin to climbing mode + // switch fix NEBSpin to climbing mode // top = replica that becomes hill climber double vmax = all[0][0]; @@ -348,7 +348,7 @@ void NEB_spin::run() top = m; } - // setup climbing NEB_spin minimization + // setup climbing NEBSpin minimization // must reinitialize minimizer so it re-creates its fix MINIMIZE if (me_universe == 0 && uscreen) @@ -402,8 +402,8 @@ void NEB_spin::run() } print_status(); - // perform climbing NEB_spin for n2steps or until replicas converge - // retrieve PE values from fix NEB_spin and print every nevery iterations + // perform climbing NEBSpin for n2steps or until replicas converge + // retrieve PE values from fix NEBSpin and print every nevery iterations // break induced if converged // damped dynamic min styles insure all replicas converge together @@ -443,7 +443,7 @@ void NEB_spin::run() initial replica does nothing ------------------------------------------------------------------------- */ -void NEB_spin::readfile(char *file, int flag) +void NEBSpin::readfile(char *file, int flag) { int i,j,m,nchunk,eofflag,nlines; tagint tag; @@ -453,7 +453,7 @@ void NEB_spin::readfile(char *file, int flag) double musp,spx,spy,spz; if (me_universe == 0 && screen) - fprintf(screen,"Reading NEB_spin coordinate file(s) ...\n"); + fprintf(screen,"Reading NEBSpin coordinate file(s) ...\n"); // flag = 0, universe root reads header of file, bcast to universe // flag = 1, each replica's root reads header of file, bcast to world @@ -645,7 +645,7 @@ void NEB_spin::readfile(char *file, int flag) interpolates between initial (spi) and final (stored in sploc) ------------------------------------------------------------------------- */ -int NEB_spin::initial_rotation(double *spi, double *sploc, double fraction) +int NEBSpin::initial_rotation(double *spi, double *sploc, double fraction) { // no interpolation for initial and final replica @@ -757,11 +757,11 @@ int NEB_spin::initial_rotation(double *spi, double *sploc, double fraction) } /* ---------------------------------------------------------------------- - universe proc 0 opens NEB_spin data file + universe proc 0 opens NEBSpin data file test if gzipped ------------------------------------------------------------------------- */ -void NEB_spin::open(char *file) +void NEBSpin::open(char *file) { compressed = 0; char *suffix = file + strlen(file) - 3; @@ -791,11 +791,11 @@ void NEB_spin::open(char *file) } /* ---------------------------------------------------------------------- - query fix NEB_spin for info on each replica - universe proc 0 prints current NEB_spin status + query fix NEBSpin for info on each replica + universe proc 0 prints current NEBSpin status ------------------------------------------------------------------------- */ -void NEB_spin::print_status() +void NEBSpin::print_status() { int nlocal = atom->nlocal; double tx,ty,tz; diff --git a/src/SPIN/neb_spin.h b/src/SPIN/neb_spin.h index 6fb36feb5d..966f617033 100644 --- a/src/SPIN/neb_spin.h +++ b/src/SPIN/neb_spin.h @@ -13,7 +13,7 @@ #ifdef COMMAND_CLASS -CommandStyle(neb/spin,NEB_spin) +CommandStyle(neb/spin,NEBSpin) #else @@ -25,13 +25,13 @@ CommandStyle(neb/spin,NEB_spin) namespace LAMMPS_NS { -class NEB_spin : protected Pointers { +class NEBSpin : protected Pointers { public: - NEB_spin(class LAMMPS *); - NEB_spin(class LAMMPS *, double, double, int, int, int, double *, double *); - ~NEB_spin(); + NEBSpin(class LAMMPS *); + NEBSpin(class LAMMPS *, double, double, int, int, int, double *, double *); + ~NEBSpin(); void command(int, char **); // process neb/spin command - void run(); // run NEB_spin + void run(); // run NEBSpin double ebf,ebr; // forward and reverse energy barriers @@ -49,7 +49,7 @@ class NEB_spin : protected Pointers { int nevery; // output interval char *infile; // name of file containing final state - class FixNEB_spin *fneb; + class FixNEBSpin *fneb; int numall; // per-replica dimension of array all double **all; // PE,plen,nlen,gradvnorm from each replica double *rdist; // normalize reaction distance, 0 to 1 @@ -69,7 +69,7 @@ class NEB_spin : protected Pointers { /* ERROR/WARNING messages: -E: NEB_spin command before simulation box is defined +E: NEBSpin command before simulation box is defined Self-explanatory. @@ -79,26 +79,26 @@ Self-explanatory. Check the input script syntax and compare to the documentation for the command. You can use -echo screen as a command-line option when running LAMMPS to see the offending line. -E: Cannot use NEB_spin with a single replica +E: Cannot use NEBSpin with a single replica Self-explanatory. -E: Cannot use NEB_spin unless atom map exists +E: Cannot use NEBSpin unless atom map exists Use the atom_modify command to create an atom map. -E: NEB_spin requires use of fix neb +E: NEBSpin requires use of fix neb Self-explanatory. -E: NEB_spin requires damped dynamics minimizer +E: NEBSpin requires damped dynamics minimizer Use a different minimization style. -E: Too many timesteps for NEB_spin +E: Too many timesteps for NEBSpin You must use a number of timesteps that fit in a 32-bit integer -for NEB_spin. +for NEBSpin. E: Too many timesteps @@ -127,12 +127,12 @@ The specified file cannot be opened. Check that the path and name are correct. If the file is a compressed file, also check that the gzip executable can be found and run. -U: Can only use NEB_spin with 1-processor replicas +U: Can only use NEBSpin with 1-processor replicas -This is current restriction for NEB_spin as implemented in LAMMPS. +This is current restriction for NEBSpin as implemented in LAMMPS. -U: Cannot use NEB_spin with atom_modify sort enabled +U: Cannot use NEBSpin with atom_modify sort enabled -This is current restriction for NEB_spin implemented in LAMMPS. +This is current restriction for NEBSpin implemented in LAMMPS. */