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changes to USER-MISC package

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This commit is contained in:
Plimpton
2021-01-21 15:37:18 -07:00
parent 4397706654
commit 54e3ee74a2
9 changed files with 74 additions and 74 deletions
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2
src/USER-MISC/fix_addtorque.cpp
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@ -47,6 +47,7 @@ FixAddTorque::FixAddTorque(LAMMPS *lmp, int narg, char **arg) :
global_freq = 1;
extscalar = 1;
extvector = 1;
energy_global_flag = 1;
dynamic_group_allow = 1;
respa_level_support = 1;
ilevel_respa = 0;
@ -97,7 +98,6 @@ int FixAddTorque::setmask()
{
int mask = 0;
mask |= POST_FORCE;
mask |= THERMO_ENERGY;
mask |= POST_FORCE_RESPA;
mask |= MIN_POST_FORCE;
return mask;

31
src/USER-MISC/fix_ffl.cpp
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@ -46,20 +46,17 @@ enum {NO_FLIP, FLIP_RESCALE, FLIP_HARD, FLIP_SOFT};
/* syntax for fix_ffl:
* fix nfix id-group ffl tau Tstart Tstop seed [flip_type]
*
* */
/* ---------------------------------------------------------------------- */
FixFFL::FixFFL(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg) {
FixFFL::FixFFL(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
{
if (narg < 7)
error->all(FLERR,"Illegal fix ffl command. Expecting: fix <fix-ID>"
" <group-ID> ffl <tau> <Tstart> <Tstop> <seed> ");
ecouple_flag = 1;
restart_peratom = 1;
time_integrate = 1;
scalar_flag = 1;
@ -121,7 +118,6 @@ FixFFL::FixFFL(LAMMPS *lmp, int narg, char **arg) :
energy = 0.0;
}
/* --- Frees up memory used by temporaries and buffers ------------------ */
FixFFL::~FixFFL() {
@ -139,14 +135,10 @@ FixFFL::~FixFFL() {
int FixFFL::setmask() {
int mask = 0;
mask |= INITIAL_INTEGRATE;
mask |= FINAL_INTEGRATE;
mask |= INITIAL_INTEGRATE_RESPA;
mask |= FINAL_INTEGRATE_RESPA;
mask |= THERMO_ENERGY;
return mask;
}
@ -181,12 +173,8 @@ void FixFFL::init_ffl() {
c1 = exp ( - gamma * 0.5 * dtv );
c2 = sqrt( (1.0 - c1*c1)* kT ); //without the mass term
}
/* ---------------------------------------------------------------------- */
void FixFFL::setup(int vflag) {
@ -199,6 +187,8 @@ void FixFFL::setup(int vflag) {
}
}
/* ---------------------------------------------------------------------- */
void FixFFL::ffl_integrate() {
double **v = atom->v;
double *rmass = atom->rmass, smi, ismi;
@ -287,9 +277,10 @@ void FixFFL::ffl_integrate() {
}
energy += deltae*0.5*force->mvv2e;
}
/* ---------------------------------------------------------------------- */
void FixFFL::initial_integrate(int /* vflag */) {
double dtfm;
@ -333,6 +324,8 @@ void FixFFL::initial_integrate(int /* vflag */) {
}
}
/* ---------------------------------------------------------------------- */
void FixFFL::final_integrate() {
double dtfm;
@ -381,6 +374,7 @@ void FixFFL::final_integrate() {
}
}
/* ---------------------------------------------------------------------- */
void FixFFL::initial_integrate_respa(int vflag, int ilevel, int /* iloop */) {
@ -398,6 +392,8 @@ void FixFFL::initial_integrate_respa(int vflag, int ilevel, int /* iloop */) {
}
}
/* ---------------------------------------------------------------------- */
void FixFFL::final_integrate_respa(int ilevel, int /* iloop */) {
dtv = step_respa[ilevel];
@ -407,6 +403,7 @@ void FixFFL::final_integrate_respa(int ilevel, int /* iloop */) {
if (ilevel==nlevels_respa-1) ffl_integrate();
}
/* ---------------------------------------------------------------------- */
double FixFFL::compute_scalar() {
@ -429,7 +426,6 @@ void *FixFFL::extract(const char *str, int &dim) {
return nullptr;
}
/* ----------------------------------------------------------------------
Called when a change to the target temperature is requested mid-run
------------------------------------------------------------------------- */
@ -459,7 +455,6 @@ double FixFFL::memory_usage() {
return bytes;
}
/* ----------------------------------------------------------------------
allocate local atom-based arrays
------------------------------------------------------------------------- */

9
src/USER-MISC/fix_flow_gauss.cpp
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@ -46,6 +46,8 @@ static const char cite_flow_gauss[] =
"pages = {189--207}\n"
"}\n\n";
/* ---------------------------------------------------------------------- */
FixFlowGauss::FixFlowGauss(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
@ -61,6 +63,7 @@ FixFlowGauss::FixFlowGauss(LAMMPS *lmp, int narg, char **arg) :
extscalar = 1;
extvector = 1;
size_vector = 3;
energy_global_flag = 1;
global_freq = 1; //data available every timestep
respa_level_support = 1;
//default respa level=outermost level is set in init()
@ -109,7 +112,6 @@ int FixFlowGauss::setmask()
{
int mask = 0;
mask |= POST_FORCE;
mask |= THERMO_ENERGY;
mask |= POST_FORCE_RESPA;
return mask;
}
@ -154,6 +156,7 @@ void FixFlowGauss::setup(int vflag)
/* ----------------------------------------------------------------------
this is where Gaussian dynamics constraint is applied
------------------------------------------------------------------------- */
void FixFlowGauss::post_force(int /*vflag*/)
{
double **f = atom->f;
@ -218,9 +221,10 @@ void FixFlowGauss::post_force(int /*vflag*/)
MPI_Allreduce(&peAdded,&pe_tmp,1,MPI_DOUBLE,MPI_SUM,world);
pe_tot += pe_tmp;
}
}
/* ---------------------------------------------------------------------- */
void FixFlowGauss::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == ilevel_respa) post_force(vflag);
@ -230,6 +234,7 @@ void FixFlowGauss::post_force_respa(int vflag, int ilevel, int /*iloop*/)
negative of work done by this fix
This is only computed if requested, either with fix_modify energy yes, or with the energy keyword. Otherwise returns 0.
------------------------------------------------------------------------- */
double FixFlowGauss::compute_scalar()
{
return -pe_tot*dt;

10
src/USER-MISC/fix_gle.cpp
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@ -30,7 +30,6 @@
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
@ -186,6 +185,8 @@ void MatrixExp(int n, const double* M, double* EM, int j=8, int k=8)
}
}
/* ---------------------------------------------------------------------- */
FixGLE::FixGLE(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
@ -193,6 +194,7 @@ FixGLE::FixGLE(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Illegal fix gle command. Expecting: fix <fix-ID>"
" <group-ID> gle <ns> <Tstart> <Tstop> <seed> <Amatrix>");
ecouple_flag = 1;
restart_peratom = 1;
time_integrate = 1;
@ -395,9 +397,6 @@ int FixGLE::setmask()
mask |= FINAL_INTEGRATE;
mask |= INITIAL_INTEGRATE_RESPA;
mask |= FINAL_INTEGRATE_RESPA;
mask |= THERMO_ENERGY;
return mask;
}
@ -499,7 +498,6 @@ void FixGLE::init_gles()
return;
}
/* ---------------------------------------------------------------------- */
void FixGLE::setup(int vflag)
@ -513,6 +511,8 @@ void FixGLE::setup(int vflag)
}
}
/* ---------------------------------------------------------------------- */
void FixGLE::gle_integrate()
{
double **v = atom->v;

2
src/USER-MISC/fix_npt_cauchy.cpp
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@ -61,6 +61,7 @@ FixNPTCauchy::FixNPTCauchy(LAMMPS *lmp, int narg, char **arg) :
if (narg < 4) error->all(FLERR,"Illegal fix npt/cauchy command");
dynamic_group_allow = 1;
ecouple_flag = 1;
time_integrate = 1;
scalar_flag = 1;
vector_flag = 1;
@ -686,7 +687,6 @@ int FixNPTCauchy::setmask()
int mask = 0;
mask |= INITIAL_INTEGRATE;
mask |= FINAL_INTEGRATE;
mask |= THERMO_ENERGY;
mask |= INITIAL_INTEGRATE_RESPA;
mask |= FINAL_INTEGRATE_RESPA;
if (pre_exchange_flag) mask |= PRE_EXCHANGE;

60
src/USER-MISC/fix_rhok.cpp
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@ -48,21 +48,19 @@ static const char cite_fix_rhok[] =
FixRhok::FixRhok( LAMMPS* inLMP, int inArgc, char** inArgv )
: Fix( inLMP, inArgc, inArgv )
{
if (lmp->citeme) lmp->citeme->add(cite_fix_rhok);
// Check arguments
if (inArgc != 8)
error->all(FLERR,"Illegal fix rhoKUmbrella command" );
if (inArgc != 8) error->all(FLERR,"Illegal fix rhoKUmbrella command" );
// Set up fix flags
scalar_flag = 1; // have compute_scalar
vector_flag = 1; // have compute_vector...
size_vector = 3; // ...with this many components
global_freq = 1; // whose value can be computed at every timestep
thermo_energy = 1; // this fix changes system's potential energy
extscalar = 0; // but the deltaPE might not scale with # of atoms
extvector = 0; // neither do the components of the vector
energy_global_flag = 1;
// Parse fix options
int n[3];
@ -79,29 +77,22 @@ FixRhok::FixRhok( LAMMPS* inLMP, int inArgc, char** inArgv )
mRhoK0 = utils::numeric(FLERR,inArgv[7],false,lmp);
}
// Methods that this fix implements
// --------------------------------
/* ---------------------------------------------------------------------- */
// Tells LAMMPS where this fix should act
int
FixRhok::setmask()
int FixRhok::setmask()
{
int mask = 0;
// This fix modifies forces...
mask |= POST_FORCE;
mask |= POST_FORCE_RESPA;
mask |= MIN_POST_FORCE;
// ...and potential energies
mask |= THERMO_ENERGY;
return mask;
}
/* ---------------------------------------------------------------------- */
// Initializes the fix at the beginning of a run
void
FixRhok::init()
void FixRhok::init()
{
// RESPA boilerplate
if (strcmp( update->integrate_style, "respa" ) == 0)
@ -121,9 +112,10 @@ FixRhok::init()
mSqrtNThis = sqrt( mNThis );
}
/* ---------------------------------------------------------------------- */
// Initial application of the fix to a system (when doing MD)
void
FixRhok::setup( int inVFlag )
void FixRhok::setup( int inVFlag )
{
if (strcmp( update->integrate_style, "verlet" ) == 0)
post_force( inVFlag );
@ -135,16 +127,20 @@ FixRhok::setup( int inVFlag )
}
}
/* ---------------------------------------------------------------------- */
// Initial application of the fix to a system (when doing minimization)
void
FixRhok::min_setup( int inVFlag )
void FixRhok::min_setup( int inVFlag )
{
post_force( inVFlag );
}
/* ---------------------------------------------------------------------- */
// Modify the forces calculated in the main force loop of ordinary MD
void
FixRhok::post_force( int /*inVFlag*/ )
void FixRhok::post_force( int /*inVFlag*/ )
{
double **x = atom->x;
double **f = atom->f;
@ -204,24 +200,27 @@ FixRhok::post_force( int /*inVFlag*/ )
}
}
/* ---------------------------------------------------------------------- */
// Forces in RESPA loop
void
FixRhok::post_force_respa( int inVFlag, int inILevel, int /*inILoop*/ )
void FixRhok::post_force_respa( int inVFlag, int inILevel, int /*inILoop*/ )
{
if (inILevel == mNLevelsRESPA - 1)
post_force( inVFlag );
}
/* ---------------------------------------------------------------------- */
// Forces in minimization loop
void
FixRhok::min_post_force( int inVFlag )
void FixRhok::min_post_force( int inVFlag )
{
post_force( inVFlag );
}
/* ---------------------------------------------------------------------- */
// Compute the change in the potential energy induced by this fix
double
FixRhok::compute_scalar()
double FixRhok::compute_scalar()
{
double rhoK = sqrt( mRhoKGlobal[0]*mRhoKGlobal[0]
+ mRhoKGlobal[1]*mRhoKGlobal[1] );
@ -229,9 +228,10 @@ FixRhok::compute_scalar()
return 0.5 * mKappa * (rhoK - mRhoK0) * (rhoK - mRhoK0);
}
/* ---------------------------------------------------------------------- */
// Compute the ith component of the vector
double
FixRhok::compute_vector( int inI )
double FixRhok::compute_vector( int inI )
{
if (inI == 0)
return mRhoKGlobal[0]; // Real part

2
src/USER-MISC/fix_ti_spring.cpp
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@ -64,6 +64,7 @@ FixTISpring::FixTISpring(LAMMPS *lmp, int narg, char **arg) :
global_freq = 1;
extscalar = 1;
extvector = 1;
energy_global_flag = 1;
// disallow resetting the time step, while this fix is defined
time_depend = 1;
@ -133,7 +134,6 @@ int FixTISpring::setmask()
mask |= POST_FORCE;
mask |= POST_FORCE_RESPA;
mask |= MIN_POST_FORCE;
mask |= THERMO_ENERGY;
return mask;
}

3
src/USER-MISC/fix_wall_region_ees.cpp
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@ -38,12 +38,14 @@ FixWallRegionEES::FixWallRegionEES(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg != 7) error->all(FLERR,"Illegal fix wall/region/ees command");
scalar_flag = 1;
vector_flag = 1;
size_vector = 3;
global_freq = 1;
extscalar = 1;
extvector = 1;
energy_global_flag = 1;
// parse args
@ -77,7 +79,6 @@ int FixWallRegionEES::setmask()
{
int mask = 0;
mask |= POST_FORCE;
mask |= THERMO_ENERGY;
mask |= POST_FORCE_RESPA;
mask |= MIN_POST_FORCE;
return mask;

25
src/fix.h
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@ -273,19 +273,18 @@ namespace FixConst {
FINAL_INTEGRATE = 1<<8,
END_OF_STEP = 1<<9,
POST_RUN = 1<<10,
//THERMO_ENERGY = 1<<11, // remove when done with refactoring
INITIAL_INTEGRATE_RESPA = 1<<12,
POST_INTEGRATE_RESPA = 1<<13,
PRE_FORCE_RESPA = 1<<14,
POST_FORCE_RESPA = 1<<15,
FINAL_INTEGRATE_RESPA = 1<<16,
MIN_PRE_EXCHANGE = 1<<17,
MIN_PRE_NEIGHBOR = 1<<18,
MIN_POST_NEIGHBOR = 1<<19,
MIN_PRE_FORCE = 1<<20,
MIN_PRE_REVERSE = 1<<21,
MIN_POST_FORCE = 1<<22,
MIN_ENERGY = 1<<23
INITIAL_INTEGRATE_RESPA = 1<<11,
POST_INTEGRATE_RESPA = 1<<12,
PRE_FORCE_RESPA = 1<<13,
POST_FORCE_RESPA = 1<<14,
FINAL_INTEGRATE_RESPA = 1<<15,
MIN_PRE_EXCHANGE = 1<<16,
MIN_PRE_NEIGHBOR = 1<<17,
MIN_POST_NEIGHBOR = 1<<18,
MIN_PRE_FORCE = 1<<19,
MIN_PRE_REVERSE = 1<<20,
MIN_POST_FORCE = 1<<21,
MIN_ENERGY = 1<<22
};
}