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cosmetic changes to comments and code structure

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This commit is contained in:
Steve Plimpton
2023-04-19 10:22:10 -06:00
parent 0f07c5e809
commit 29ad47cc0f
7 changed files with 109 additions and 97 deletions
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5
doc/src/fix_mdi_qm.rst
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@ -294,7 +294,10 @@ LAMMPS can also be used as an MDI driver in other unit choices it
supports, e.g. *lj*, but then no unit conversion to MDI units is
performed.
If this fix is used in conjuction with a QM code that does not support periodic boundary conditions (more specifically, a QM code that does not support the ``>CELL`` MDI command), the LAMMPS input file must specify non-periodic boundary conditions.
If this fix is used in conjuction with a QM code that does not support
periodic boundary conditions (more specifically, a QM code that does
not support the ``>CELL`` MDI command), the LAMMPS system must be
fully non-periodic. I.e. no dimension of the system can be periodic.
Related commands
""""""""""""""""

5
doc/src/fix_mdi_qmmm.rst
View File

@ -261,7 +261,10 @@ used to specify *real* or *metal* units. This will ensure the correct
unit conversions between LAMMPS and MDI units. The other code will
also perform similar unit conversions into its preferred units.
If this fix is used in conjuction with a QM code that does not support periodic boundary conditions (more specifically, a QM code that does not support the ``>CELL`` MDI command), the LAMMPS input file must specify non-periodic boundary conditions.
If this fix is used in conjuction with a QM code that does not support
periodic boundary conditions (more specifically, a QM code that does
not support the ``>CELL`` MDI command), the LAMMPS system must be
fully non-periodic. I.e. no dimension of the system can be periodic.
Related commands
""""""""""""""""

84
src/MDI/fix_mdi_qm.cpp
View File

@ -512,35 +512,11 @@ void FixMDIQM::post_force(int vflag)
ierr = MDI_Send(&xqm[0][0], 3 * nqm, MDI_DOUBLE, mdicomm);
if (ierr) error->all(FLERR, "MDI: >COORDS data");
// request potential energy from MDI engine
// request QM energy from MDI engine
// this triggers engine to perform QM calculation
// qm_energy = fix output for global QM energy
// sets qm_energy = fix output for global QM energy
if (pe_exists && keelec_exists) {
int pe_energy, keelec_energy;
// get the total potential energy
ierr = MDI_Send_command("<PE", mdicomm);
if (ierr) error->all(FLERR, "MDI: <PE command");
ierr = MDI_Recv(&pe_energy, 1, MDI_DOUBLE, mdicomm);
if (ierr) error->all(FLERR, "MDI: <PE data");
// get the kinetic energy of the electrons
ierr = MDI_Send_command("<KE_ELEC", mdicomm);
if (ierr) error->all(FLERR, "MDI: <KE_ELEC command");
ierr = MDI_Recv(&keelec_energy, 1, MDI_DOUBLE, mdicomm);
if (ierr) error->all(FLERR, "MDI: <KE_ELEC data");
qm_energy = pe_energy + keelec_energy;
} else {
// get the total energy
ierr = MDI_Send_command("<ENERGY", mdicomm);
if (ierr) error->all(FLERR, "MDI: <ENERGY command");
ierr = MDI_Recv(&qm_energy, 1, MDI_DOUBLE, mdicomm);
if (ierr) error->all(FLERR, "MDI: <ENERGY data");
}
MPI_Bcast(&qm_energy, 1, MPI_DOUBLE, 0, world);
qm_energy *= mdi2lmp_energy;
request_qm_energy();
// request forces from MDI engine
@ -1008,9 +984,9 @@ void FixMDIQM::send_box()
{
int ierr;
// Only send the cell dimensions if this is a periodic simulation
if (domain->xperiodic == 1 && domain->yperiodic == 1 && domain->zperiodic == 1) {
// only send cell dimensions if fully periodic simulation
if (domain->nonperiodic == 0) {
if (celldispl_exists) {
ierr = MDI_Send_command(">CELL_DISPL", mdicomm);
if (ierr) error->all(FLERR, "MDI: >CELL_DISPL command");
@ -1023,17 +999,49 @@ void FixMDIQM::send_box()
ierr = MDI_Send(qm_cell, 9, MDI_DOUBLE, mdicomm);
if (ierr) error->all(FLERR, "MDI: >CELL data");
} else {
if (domain->xperiodic == 1 || domain->yperiodic == 1 || domain->zperiodic == 1) {
error->all(FLERR,
"MDI: The QM driver does not work for simulations with both periodic and "
"non-periodic dimensions.");
}
} else if (domain->xperiodic == 1 || domain->yperiodic == 1 ||
domain->zperiodic == 1) {
error->all(FLERR,"MDI requires fully periodic or fully non-periodic system");
}
}
/* ----------------------------------------------------------------------
request QM energy from MDI engine
set qm_energy = fix output for global QM energy
------------------------------------------------------------------------- */
void FixMDIQM::request_qm_energy()
{
int ierr;
// QM energy = <PE + <KE_ELEC or <ENERGY, depending on engine options
if (pe_exists && keelec_exists) {
int pe_energy, keelec_energy;
ierr = MDI_Send_command("<PE", mdicomm);
if (ierr) error->all(FLERR, "MDI: <PE command");
ierr = MDI_Recv(&pe_energy, 1, MDI_DOUBLE, mdicomm);
if (ierr) error->all(FLERR, "MDI: <PE data");
ierr = MDI_Send_command("<KE_ELEC", mdicomm);
if (ierr) error->all(FLERR, "MDI: <KE_ELEC command");
ierr = MDI_Recv(&keelec_energy, 1, MDI_DOUBLE, mdicomm);
if (ierr) error->all(FLERR, "MDI: <KE_ELEC data");
qm_energy = pe_energy + keelec_energy;
} else {
ierr = MDI_Send_command("<ENERGY", mdicomm);
if (ierr) error->all(FLERR, "MDI: <ENERGY command");
ierr = MDI_Recv(&qm_energy, 1, MDI_DOUBLE, mdicomm);
if (ierr) error->all(FLERR, "MDI: <ENERGY data");
}
MPI_Bcast(&qm_energy, 1, MPI_DOUBLE, 0, world);
qm_energy *= mdi2lmp_energy;
}
/* ----------------------------------------------------------------------
MDI to/from LAMMPS conversion factors
------------------------------------------------------------------------- */

2
src/MDI/fix_mdi_qm.h
View File

@ -105,6 +105,8 @@ class FixMDIQM : public Fix {
void send_elements();
void send_box();
void request_qm_energy();
void unit_conversions();
};

101
src/MDI/fix_mdi_qmmm.cpp
View File

@ -726,11 +726,11 @@ void FixMDIQMMM::pre_force(int vflag)
ierr = MDI_Send(qpotential, nqm, MDI_DOUBLE, mdicomm);
if (ierr) error->all(FLERR, "MDI: >POTENTIAL_AT_NUCLEI data");
// request QM potential energy from MDI engine
// request QM energy from MDI engine
// this triggers engine to perform QM calculation
// qm_energy = fix output for global QM energy
// sets qm_energy = fix output for global QM energy
get_qm_energy();
request_qm_energy();
// request forces on QM atoms from MDI engine
@ -886,11 +886,11 @@ void FixMDIQMMM::post_force_direct(int vflag)
ierr = MDI_Send(&xmm[0][0], 3 * nmm, MDI_DOUBLE, mdicomm);
if (ierr) error->all(FLERR, "MDI: >CLATTICE data");
// request QM potential energy from MDI engine
// request QM energy from MDI engine
// this triggers engine to perform QM calculation
// qm_energy = fix output for global QM energy
// sets qm_energy = fix output for global QM energy
get_qm_energy();
request_qm_energy();
// request forces on QM atoms from MDI engine
@ -1767,9 +1767,9 @@ void FixMDIQMMM::send_box()
{
int ierr;
// Only send the cell dimensions if this is a periodic simulation
if (domain->xperiodic == 1 && domain->yperiodic == 1 && domain->zperiodic == 1) {
// only send cell dimensions if fully periodic simulation
if (domain->nonperiodic == 0) {
if (celldispl_exists) {
ierr = MDI_Send_command(">CELL_DISPL", mdicomm);
if (ierr) error->all(FLERR, "MDI: >CELL_DISPL command");
@ -1782,52 +1782,12 @@ void FixMDIQMMM::send_box()
ierr = MDI_Send(qm_cell, 9, MDI_DOUBLE, mdicomm);
if (ierr) error->all(FLERR, "MDI: >CELL data");
} else {
if (domain->xperiodic == 1 || domain->yperiodic == 1 || domain->zperiodic == 1) {
error->all(FLERR,
"MDI: The QM driver does not work for simulations with both periodic and "
"non-periodic dimensions.");
}
} else if (domain->xperiodic == 1 || domain->yperiodic == 1 ||
domain->zperiodic == 1) {
error->all(FLERR,"MDI requires fully periodic or fully non-periodic system");
}
}
/* ----------------------------------------------------------------------
get the energy of the QM system
------------------------------------------------------------------------- */
void FixMDIQMMM::get_qm_energy()
{
int ierr;
if (pe_exists && keelec_exists) {
int pe_energy, keelec_energy;
// get the total potential energy
ierr = MDI_Send_command("<PE", mdicomm);
if (ierr) error->all(FLERR, "MDI: <PE command");
ierr = MDI_Recv(&pe_energy, 1, MDI_DOUBLE, mdicomm);
if (ierr) error->all(FLERR, "MDI: <PE data");
// get the kinetic energy of the electrons
ierr = MDI_Send_command("<KE_ELEC", mdicomm);
if (ierr) error->all(FLERR, "MDI: <KE_ELEC command");
ierr = MDI_Recv(&keelec_energy, 1, MDI_DOUBLE, mdicomm);
if (ierr) error->all(FLERR, "MDI: <KE_ELEC data");
qm_energy = pe_energy + keelec_energy;
} else {
// get the total energy
ierr = MDI_Send_command("<ENERGY", mdicomm);
if (ierr) error->all(FLERR, "MDI: <ENERGY command");
ierr = MDI_Recv(&qm_energy, 1, MDI_DOUBLE, mdicomm);
if (ierr) error->all(FLERR, "MDI: <ENERGY data");
}
MPI_Bcast(&qm_energy, 1, MPI_DOUBLE, 0, world);
qm_energy *= mdi2lmp_energy;
}
/* ----------------------------------------------------------------------
send LAMMPS MM atom count to MDI engine
------------------------------------------------------------------------- */
@ -1876,6 +1836,43 @@ void FixMDIQMMM::send_charges_mm()
if (ierr) error->all(FLERR, "MDI: >LATTICE data");
}
/* ----------------------------------------------------------------------
request QM energy from MDI engine
set qm_energy = fix output for global QM energy
------------------------------------------------------------------------- */
void FixMDIQMMM::request_qm_energy()
{
int ierr;
// QM energy = <PE + <KE_ELEC or <ENERGY, depending on engine options
if (pe_exists && keelec_exists) {
int pe_energy, keelec_energy;
ierr = MDI_Send_command("<PE", mdicomm);
if (ierr) error->all(FLERR, "MDI: <PE command");
ierr = MDI_Recv(&pe_energy, 1, MDI_DOUBLE, mdicomm);
if (ierr) error->all(FLERR, "MDI: <PE data");
ierr = MDI_Send_command("<KE_ELEC", mdicomm);
if (ierr) error->all(FLERR, "MDI: <KE_ELEC command");
ierr = MDI_Recv(&keelec_energy, 1, MDI_DOUBLE, mdicomm);
if (ierr) error->all(FLERR, "MDI: <KE_ELEC data");
qm_energy = pe_energy + keelec_energy;
} else {
ierr = MDI_Send_command("<ENERGY", mdicomm);
if (ierr) error->all(FLERR, "MDI: <ENERGY command");
ierr = MDI_Recv(&qm_energy, 1, MDI_DOUBLE, mdicomm);
if (ierr) error->all(FLERR, "MDI: <ENERGY data");
}
MPI_Bcast(&qm_energy, 1, MPI_DOUBLE, 0, world);
qm_energy *= mdi2lmp_energy;
}
/* ----------------------------------------------------------------------
MDI to/from LAMMPS conversion factors
------------------------------------------------------------------------- */

2
src/MDI/fix_mdi_qmmm.h
View File

@ -156,7 +156,7 @@ class FixMDIQMMM : public Fix {
void send_elements_mm();
void send_charges_mm();
void get_qm_energy();
void request_qm_energy();
void unit_conversions();
};

7
src/MDI/mdi_engine.cpp
View File

@ -1533,10 +1533,9 @@ void MDIEngine::send_pe()
/* ----------------------------------------------------------------------
<KE_ELEC command
send the kinetic energy of the electrons
because lammps does not model electrons explicitly, this is zero
this is primarily for use when LAMMPS is filling a role that would
normally be filled by a QM code
send kinetic energy of the electrons
zero for LAMMPS, because it does not model electrons explicitly
for compatibiity with QM engines which support this command
---------------------------------------------------------------------- */
void MDIEngine::send_ke_elec()