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rename 2 version to regular version

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This commit is contained in:
Steve Plimpton
2021-09-23 12:55:28 -06:00
parent 8b69b232a8
commit c855c6f0ab
5 changed files with 65 additions and 65 deletions
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18
src/MDI/fix_mdi_engine2.cpp → src/MDI/fix_mdi_engine.cpp
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@ -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");
}

14
src/MDI/fix_mdi_engine2.h → src/MDI/fix_mdi_engine.h
View File

@ -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();

10
src/MDI/library_mdi.cpp
View File

@ -23,7 +23,7 @@
#define LAMMPS_LIB_MPI 1
#include "library.h"
#include "fix_mdi_engine_old.h"
#include "mdi_engine.h"
#include <cstring>
@ -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);
}

74
src/MDI/mdi_engine2.cpp → src/MDI/mdi_engine.cpp
View File

@ -16,7 +16,7 @@
MolSSI Driver Interface (MDI) support for LAMMPS
------------------------------------------------------------------------- */
#include "mdi_engine2.h"
#include "mdi_engine.h"
#include <limits>
#include <cstring>
@ -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<FixMDIEngine2 *>(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<FixMDIEngine *>(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;

14
src/MDI/mdi_engine2.h → src/MDI/mdi_engine.h
View File

@ -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;