diff --git a/src/MDI/fix_mdi_engine2.cpp b/src/MDI/fix_mdi_engine.cpp similarity index 84% rename from src/MDI/fix_mdi_engine2.cpp rename to src/MDI/fix_mdi_engine.cpp index 27d0ed3785..21df468c40 100644 --- a/src/MDI/fix_mdi_engine2.cpp +++ b/src/MDI/fix_mdi_engine.cpp @@ -17,15 +17,15 @@ ------------------------------------------------------------------------- */ #include "error.h" -#include "fix_mdi_engine2.h" -#include "mdi_engine2.h" +#include "fix_mdi_engine.h" +#include "mdi_engine.h" using namespace LAMMPS_NS; using namespace FixConst; /* ---------------------------------------------------------------------- */ -FixMDIEngine2::FixMDIEngine2(LAMMPS *lmp, int narg, char **arg) : +FixMDIEngine::FixMDIEngine(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) { if (narg != 3) error->all(FLERR, "Illegal fix mdi/engine command"); @@ -33,7 +33,7 @@ FixMDIEngine2::FixMDIEngine2(LAMMPS *lmp, int narg, char **arg) : /* ---------------------------------------------------------------------- */ -int FixMDIEngine2::setmask() +int FixMDIEngine::setmask() { int mask = 0; mask |= POST_INTEGRATE; @@ -46,35 +46,35 @@ int FixMDIEngine2::setmask() /* ---------------------------------------------------------------------- */ -void FixMDIEngine2::post_integrate() +void FixMDIEngine::post_integrate() { mdi_engine->engine_node("@COORDS"); } /* ---------------------------------------------------------------------- */ -void FixMDIEngine2::min_pre_force(int vflag) +void FixMDIEngine::min_pre_force(int vflag) { mdi_engine->engine_node("@COORDS"); } /* ---------------------------------------------------------------------- */ -void FixMDIEngine2::post_force(int vflag) +void FixMDIEngine::post_force(int vflag) { mdi_engine->engine_node("@FORCES"); } /* ---------------------------------------------------------------------- */ -void FixMDIEngine2::min_post_force(int vflag) +void FixMDIEngine::min_post_force(int vflag) { mdi_engine->engine_node("@FORCES"); } /* ---------------------------------------------------------------------- */ -void FixMDIEngine2::end_of_step() +void FixMDIEngine::end_of_step() { mdi_engine->engine_node("@ENDSTEP"); } diff --git a/src/MDI/fix_mdi_engine2.h b/src/MDI/fix_mdi_engine.h similarity index 87% rename from src/MDI/fix_mdi_engine2.h rename to src/MDI/fix_mdi_engine.h index 2a9cabb7fc..c8a2ca7cdf 100644 --- a/src/MDI/fix_mdi_engine2.h +++ b/src/MDI/fix_mdi_engine.h @@ -13,23 +13,23 @@ #ifdef FIX_CLASS // clang-format off -FixStyle(mdi/engine2, FixMDIEngine2); +FixStyle(mdi/engine, FixMDIEngine); // clang-format on #else -#ifndef LMP_FIX_MDI_ENGINE2_H -#define LMP_FIX_MDI_ENGINE2_H +#ifndef LMP_FIX_MDI_ENGINE_H +#define LMP_FIX_MDI_ENGINE_H #include "fix.h" namespace LAMMPS_NS { -class FixMDIEngine2 : public Fix { +class FixMDIEngine : public Fix { public: - class MDIEngine2 *mdi_engine; + class MDIEngine *mdi_engine; - FixMDIEngine2(class LAMMPS *, int, char **); - ~FixMDIEngine2() {} + FixMDIEngine(class LAMMPS *, int, char **); + ~FixMDIEngine() {} int setmask(); void init() {} void post_integrate(); diff --git a/src/MDI/library_mdi.cpp b/src/MDI/library_mdi.cpp index d5489207a4..70bb825767 100644 --- a/src/MDI/library_mdi.cpp +++ b/src/MDI/library_mdi.cpp @@ -23,7 +23,7 @@ #define LAMMPS_LIB_MPI 1 #include "library.h" -#include "fix_mdi_engine_old.h" +#include "mdi_engine.h" #include @@ -122,9 +122,9 @@ The function executes a single command from an external MDI driver. int lammps_execute_mdi_command(const char *command, MDI_Comm comm, void *class_obj) { - FixMDIEngineOld *mdi_fix = (FixMDIEngineOld *) class_obj; - return mdi_fix->execute_command(command, comm); + //FixMDIEngineOld *mdi_fix = (FixMDIEngineOld *) class_obj; + //return mdi_fix->execute_command(command, comm); - //MDIEngine2 *mdi_engine = (MDIEngine2 *) class_obj; - //return mdi_engine->execute_command(command, comm); + MDIEngine *mdi_engine = (MDIEngine *) class_obj; + return mdi_engine->execute_command(command,comm); } diff --git a/src/MDI/mdi_engine2.cpp b/src/MDI/mdi_engine.cpp similarity index 97% rename from src/MDI/mdi_engine2.cpp rename to src/MDI/mdi_engine.cpp index b486dfe52f..f9a9fd5747 100644 --- a/src/MDI/mdi_engine2.cpp +++ b/src/MDI/mdi_engine.cpp @@ -16,7 +16,7 @@ MolSSI Driver Interface (MDI) support for LAMMPS ------------------------------------------------------------------------- */ -#include "mdi_engine2.h" +#include "mdi_engine.h" #include #include @@ -25,7 +25,7 @@ #include "compute.h" #include "domain.h" #include "error.h" -#include "fix_mdi_engine2.h" +#include "fix_mdi_engine.h" #include "force.h" #include "group.h" #include "input.h" @@ -62,7 +62,7 @@ enum{CREATE_ATOM,CREATE_ID,CREATE_TYPE,CREATE_X,CREATE_V,CREATE_IMAGE,CREATE_GO} NOTE: may later have other MDI command variants? ---------------------------------------------------------------------- */ -void MDIEngine2::command(int narg, char **arg) +void MDIEngine::command(int narg, char **arg) { if (narg < 1) error->all(FLERR,"Illegal mdi command"); @@ -79,7 +79,7 @@ void MDIEngine2::command(int narg, char **arg) when EXIT command is received, mdi engine command exits ---------------------------------------------------------------------- */ -void MDIEngine2::mdi_engine(int narg, char **arg) +void MDIEngine::mdi_engine(int narg, char **arg) { if (narg > 0) error->all(FLERR,"Illegal mdi engine command"); @@ -221,7 +221,7 @@ void MDIEngine2::mdi_engine(int narg, char **arg) return when not the case or EXIT command received ---------------------------------------------------------------------- */ -void MDIEngine2::engine_node(const char *node) +void MDIEngine::engine_node(const char *node) { int ierr; @@ -268,7 +268,7 @@ void MDIEngine2::engine_node(const char *node) when LAMMPS is running as a plugin ---------------------------------------------------------------------- */ -int MDIEngine2::execute_command(const char *command, MDI_Comm mdicomm) +int MDIEngine::execute_command(const char *command, MDI_Comm mdicomm) { int ierr; @@ -479,7 +479,7 @@ int MDIEngine2::execute_command(const char *command, MDI_Comm mdicomm) standard MDI commands and custom LAMMPS commands ---------------------------------------------------------------------- */ -void MDIEngine2::mdi_commands() +void MDIEngine::mdi_commands() { // ------------------------------------ // commands and nodes that an MDI-compliant MD code supports @@ -661,7 +661,7 @@ void MDIEngine2::mdi_commands() run MD simulation under control of driver one step at a time ---------------------------------------------------------------------- */ -void MDIEngine2::mdi_md() +void MDIEngine::mdi_md() { //int ifix = modify->find_fix_by_style("mdi/engine2"); //bool added_mdi_engine_fix = false; @@ -672,9 +672,9 @@ void MDIEngine2::mdi_md() // remove mdi/engine fix this method instantiated //modify->delete_fix("MDI_ENGINE_INTERNAL"); - modify->add_fix("MDI_ENGINE_INTERNAL all mdi/engine2"); - int ifix = modify->find_fix_by_style("mdi/engine2"); - mdi_fix = static_cast(modify->fix[ifix]); + modify->add_fix("MDI_ENGINE_INTERNAL all mdi/engine"); + int ifix = modify->find_fix_by_style("mdi/engine"); + mdi_fix = static_cast(modify->fix[ifix]); mdi_fix->mdi_engine = this; // initialize a new MD simulation @@ -726,7 +726,7 @@ void MDIEngine2::mdi_md() perform minimization under control of driver ---------------------------------------------------------------------- */ -void MDIEngine2::mdi_optg() +void MDIEngine::mdi_optg() { // initialize an energy minization @@ -787,7 +787,7 @@ void MDIEngine2::mdi_optg() assumes all atoms already exist ---------------------------------------------------------------------- */ -void MDIEngine2::receive_double1(int which) +void MDIEngine::receive_double1(int which) { reallocate(); @@ -819,7 +819,7 @@ void MDIEngine2::receive_double1(int which) assumes all atoms already exist ---------------------------------------------------------------------- */ -void MDIEngine2::receive_int1(int which) +void MDIEngine::receive_int1(int which) { reallocate(); @@ -852,7 +852,7 @@ void MDIEngine2::receive_int1(int which) for which = COORD, assumes atom displacement is small ---------------------------------------------------------------------- */ -void MDIEngine2::receive_double3(int which, int addflag) +void MDIEngine::receive_double3(int which, int addflag) { reallocate(); @@ -924,7 +924,7 @@ void MDIEngine2::receive_double3(int which, int addflag) atoms are ordered by atomID, 1 to Natoms ---------------------------------------------------------------------- */ -void MDIEngine2::send_double1(int which) +void MDIEngine::send_double1(int which) { reallocate(); memset(buf1,0,atom->natoms*sizeof(double)); @@ -971,7 +971,7 @@ void MDIEngine2::send_double1(int which) atoms are ordered by atomID, 1 to Natoms ---------------------------------------------------------------------- */ -void MDIEngine2::send_int1(int which) +void MDIEngine::send_int1(int which) { reallocate(); memset(ibuf1,0,atom->natoms*sizeof(int)); @@ -1003,7 +1003,7 @@ void MDIEngine2::send_int1(int which) atoms are ordered by atomID, 1 to Natoms ---------------------------------------------------------------------- */ -void MDIEngine2::send_double3(int which) +void MDIEngine::send_double3(int which) { reallocate(); memset(buf3,0,3*atom->natoms*sizeof(double)); @@ -1045,7 +1045,7 @@ void MDIEngine2::send_double3(int which) atoms are ordered by atomID, 1 to Natoms ---------------------------------------------------------------------- */ -void MDIEngine2::send_labels() +void MDIEngine::send_labels() { char *labels = new char[atom->natoms * MDI_LABEL_LENGTH]; memset(labels,' ',atom->natoms * MDI_LABEL_LENGTH); @@ -1069,7 +1069,7 @@ void MDIEngine2::send_labels() send total energy = PE + KE ---------------------------------------------------------------------- */ -void MDIEngine2::send_total_energy() +void MDIEngine::send_total_energy() { double potential_energy = pe->compute_scalar(); double kinetic_energy = ke->compute_scalar(); @@ -1085,7 +1085,7 @@ void MDIEngine2::send_total_energy() send potential energy ---------------------------------------------------------------------- */ -void MDIEngine2::send_pe() +void MDIEngine::send_pe() { double potential_energy = pe->compute_scalar(); potential_energy *= lmp2mdi_energy; @@ -1099,7 +1099,7 @@ void MDIEngine2::send_pe() send kinetic energy ---------------------------------------------------------------------- */ -void MDIEngine2::send_ke() +void MDIEngine::send_ke() { double kinetic_energy = ke->compute_scalar(); kinetic_energy *= lmp2mdi_energy; @@ -1113,7 +1113,7 @@ void MDIEngine2::send_ke() send simulation box edge vectors ---------------------------------------------------------------------- */ -void MDIEngine2::send_cell() +void MDIEngine::send_cell() { double celldata[9]; @@ -1140,7 +1140,7 @@ void MDIEngine2::send_cell() in conjunction with >CELL_DISPL this can adjust box arbitrarily ---------------------------------------------------------------------- */ -void MDIEngine2::receive_cell() +void MDIEngine::receive_cell() { double celldata[9]; @@ -1183,7 +1183,7 @@ void MDIEngine2::receive_cell() send simulation box origin = lower-left corner ---------------------------------------------------------------------- */ -void MDIEngine2::send_celldispl() +void MDIEngine::send_celldispl() { double celldata[3]; @@ -1203,7 +1203,7 @@ void MDIEngine2::send_celldispl() reset simulation box origin = lower-left corner ---------------------------------------------------------------------- */ -void MDIEngine2::receive_celldispl() +void MDIEngine::receive_celldispl() { double celldata[3]; int ierr = MDI_Recv(celldata,3,MDI_DOUBLE,mdicomm); @@ -1253,7 +1253,7 @@ void MDIEngine2::receive_celldispl() for use by a subsequent command, e.g. ones that send strings ---------------------------------------------------------------------- */ -void MDIEngine2::nbytes_command() +void MDIEngine::nbytes_command() { int ierr = MDI_Recv(&nbytes,1,MDI_INT,mdicomm); if (ierr) error->all(FLERR,"MDI: NBYTES data"); @@ -1266,7 +1266,7 @@ void MDIEngine2::nbytes_command() invoke as a LAMMPS command ---------------------------------------------------------------------- */ -void MDIEngine2::single_command() +void MDIEngine::single_command() { if (nbytes < 0) error->all(FLERR,"MDI: COMMAND nbytes has not been set"); @@ -1287,7 +1287,7 @@ void MDIEngine2::single_command() invoke as multiple LAMMPS commands ---------------------------------------------------------------------- */ -void MDIEngine2::many_commands() +void MDIEngine::many_commands() { if (nbytes < 0) error->all(FLERR,"MDI: COMMANDS nbytes has not been set"); @@ -1308,7 +1308,7 @@ void MDIEngine2::many_commands() invoke as a LAMMPS input script ---------------------------------------------------------------------- */ -void MDIEngine2::infile() +void MDIEngine::infile() { if (nbytes < 0) error->all(FLERR,"MDI: INFILE nbytes has not been set"); @@ -1335,7 +1335,7 @@ void MDIEngine2::infile() this method does NOT increment timestep ---------------------------------------------------------------------- */ -void MDIEngine2::evaluate() +void MDIEngine::evaluate() { if (neighbor->ago < 0) { @@ -1371,7 +1371,7 @@ void MDIEngine2::evaluate() allows caller to define a new simulation box ---------------------------------------------------------------------- */ -void MDIEngine2::reset_box() +void MDIEngine::reset_box() { int ierr; double values[9]; @@ -1396,7 +1396,7 @@ void MDIEngine2::reset_box() assumes current atom->natoms set by >NATOMS command is correct ---------------------------------------------------------------------- */ -void MDIEngine2::create_atoms(int flag) +void MDIEngine::create_atoms(int flag) { int ierr; @@ -1497,7 +1497,7 @@ void MDIEngine2::create_atoms(int flag) send scalar pressure value ---------------------------------------------------------------------- */ -void MDIEngine2::send_pressure() +void MDIEngine::send_pressure() { double pressure = press->compute_scalar(); pressure *= lmp2mdi_pressure; @@ -1511,7 +1511,7 @@ void MDIEngine2::send_pressure() send 6-component pressure tensor ---------------------------------------------------------------------- */ -void MDIEngine2::send_ptensor() +void MDIEngine::send_ptensor() { double ptensor[6]; press->compute_vector(); @@ -1532,7 +1532,7 @@ void MDIEngine2::send_ptensor() reallocate storage for all atoms if necessary ------------------------------------------------------------------------- */ -void MDIEngine2::reallocate() +void MDIEngine::reallocate() { if (atom->natoms <= maxbuf) return; @@ -1562,7 +1562,7 @@ void MDIEngine2::reallocate() MDI to/from LAMMPS conversion factors ------------------------------------------------------------------------- */ -void MDIEngine2::unit_conversions() +void MDIEngine::unit_conversions() { double angstrom_to_bohr,kelvin_to_hartree,ev_to_hartree; diff --git a/src/MDI/mdi_engine2.h b/src/MDI/mdi_engine.h similarity index 93% rename from src/MDI/mdi_engine2.h rename to src/MDI/mdi_engine.h index edf6be7cfb..b99db49107 100644 --- a/src/MDI/mdi_engine2.h +++ b/src/MDI/mdi_engine.h @@ -13,22 +13,22 @@ #ifdef COMMAND_CLASS // clang-format off -CommandStyle(mdi,MDIEngine2); +CommandStyle(mdi,MDIEngine); // clang-format on #else -#ifndef LMP_MDI_ENGINE2_H -#define LMP_MDI_ENGINE2_H +#ifndef LMP_MDI_ENGINE_H +#define LMP_MDI_ENGINE_H #include "command.h" #include "mdi.h" namespace LAMMPS_NS { -class MDIEngine2 : public Command { +class MDIEngine : public Command { public: - MDIEngine2(LAMMPS *lmp) : Command(lmp) {} - virtual ~MDIEngine2() {} + MDIEngine(LAMMPS *lmp) : Command(lmp) {} + virtual ~MDIEngine() {} void command(int, char **); int execute_command(const char *command, MDI_Comm mdicomm); @@ -48,7 +48,7 @@ class MDIEngine2 : public Command { bool exit_command; // true if EXIT command received from driver MDI_Comm mdicomm; - class FixMDIEngine2 *mdi_fix; + class FixMDIEngine *mdi_fix; char *id_ke,*id_pe,*id_press; class Irregular *irregular;