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renaming of variables and command names in USER-SPH

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This commit is contained in:
Steve Plimpton
2020-04-30 16:40:09 -06:00
parent 5ec357adfc
commit 4eb4839f6d
29 changed files with 318 additions and 286 deletions
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47
src/atom.cpp
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@ -73,8 +73,8 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
nperatom = maxperatom = 0;
peratom = NULL;
// initialize atom arrays
// customize by adding new array
// --------------------------------------------------------------------
// 1st customization section: customize by adding new per-atom variables
tag = NULL;
type = mask = NULL;
@ -159,9 +159,12 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
// USER-SPH package
rho = drho = e = de = cv = NULL;
rho = drho = esph = desph = cv = NULL;
vest = NULL;
// end of customization section
// --------------------------------------------------------------------
// user-defined molecules
nmolecule = 0;
@ -240,8 +243,9 @@ Atom::~Atom()
delete [] peratom[i].name;
memory->sfree(peratom);
// --------------------------------------------------------------------
// 2nd customization section: customize by adding new per-atom variables
// delete atom arrays
// customize by adding new array
memory->destroy(tag);
memory->destroy(type);
@ -287,8 +291,8 @@ Atom::~Atom()
memory->destroy(rho);
memory->destroy(drho);
memory->destroy(e);
memory->destroy(de);
memory->destroy(esph);
memory->destroy(desph);
memory->destroy(cv);
memory->destroy(vest);
@ -340,6 +344,9 @@ Atom::~Atom()
memory->destroy(improper_atom3);
memory->destroy(improper_atom4);
// end of customization section
// --------------------------------------------------------------------
// delete custom atom arrays
for (int i = 0; i < nivector; i++) {
@ -411,7 +418,8 @@ void Atom::peratom_create()
peratom = NULL;
nperatom = maxperatom = 0;
// customize: add new peratom variables here, order does not matter
// --------------------------------------------------------------------
// 3rd customization section: add peratom variables here, order does not matter
// register tagint & imageint variables as INT or BIGINT
int tagintsize = INT;
@ -541,8 +549,8 @@ void Atom::peratom_create()
add_peratom("rho",&rho,DOUBLE,0);
add_peratom("drho",&drho,DOUBLE,0,1); // set per-thread flag
add_peratom("e",&e,DOUBLE,0);
add_peratom("de",&de,DOUBLE,0,1); // set per-thread flag
add_peratom("esph",&esph,DOUBLE,0);
add_peratom("desph",&desph,DOUBLE,0,1); // set per-thread flag
add_peratom("vest",&vest,DOUBLE,3);
add_peratom("cv",&cv,DOUBLE,0);
@ -554,6 +562,9 @@ void Atom::peratom_create()
add_peratom("eff_plastic_strain",&eff_plastic_strain,DOUBLE,0);
add_peratom("eff_plastic_strain_rate",&eff_plastic_strain_rate,DOUBLE,0);
add_peratom("damage",&damage,DOUBLE,0);
// end of customization section
// --------------------------------------------------------------------
}
/* ----------------------------------------------------------------------
@ -636,11 +647,14 @@ void Atom::add_peratom_vary(const char *name, void *address,
/* ----------------------------------------------------------------------
add info for a single per-atom array to PerAtom data struct
customize by adding new flag, identical list as atom.h 2nd customization
------------------------------------------------------------------------- */
void Atom::set_atomflag_defaults()
{
// --------------------------------------------------------------------
// 4th customization section: customize by adding new flag
// identical list as 2nd customization in atom.h
sphere_flag = ellipsoid_flag = line_flag = tri_flag = body_flag = 0;
peri_flag = electron_flag = 0;
wavepacket_flag = sph_flag = 0;
@ -649,7 +663,7 @@ void Atom::set_atomflag_defaults()
rmass_flag = radius_flag = omega_flag = torque_flag = angmom_flag = 0;
vfrac_flag = spin_flag = eradius_flag = ervel_flag = erforce_flag = 0;
cs_flag = csforce_flag = vforce_flag = ervelforce_flag = etag_flag = 0;
rho_flag = e_flag = cv_flag = vest_flag = 0;
rho_flag = esph_flag = cv_flag = vest_flag = 0;
dpd_flag = edpd_flag = tdpd_flag = 0;
sp_flag = 0;
x0_flag = 0;
@ -2472,11 +2486,13 @@ void Atom::remove_custom(int flag, int index)
/* ----------------------------------------------------------------------
return a pointer to a named internal variable
if don't recognize name, return NULL
customize by adding names
------------------------------------------------------------------------- */
void *Atom::extract(char *name)
{
// --------------------------------------------------------------------
// 5th customization section: customize by adding new variable name
if (strcmp(name,"mass") == 0) return (void *) mass;
if (strcmp(name,"id") == 0) return (void *) tag;
@ -2514,8 +2530,8 @@ void *Atom::extract(char *name)
if (strcmp(name,"rho") == 0) return (void *) rho;
if (strcmp(name,"drho") == 0) return (void *) drho;
if (strcmp(name,"e") == 0) return (void *) e;
if (strcmp(name,"de") == 0) return (void *) de;
if (strcmp(name,"esph") == 0) return (void *) esph;
if (strcmp(name,"desph") == 0) return (void *) desph;
if (strcmp(name,"cv") == 0) return (void *) cv;
if (strcmp(name,"vest") == 0) return (void *) vest;
@ -2531,6 +2547,9 @@ void *Atom::extract(char *name)
if (strcmp(name,"dpdTheta") == 0) return (void *) dpdTheta;
if (strcmp(name,"edpd_temp") == 0) return (void *) edpd_temp;
// end of customization section
// --------------------------------------------------------------------
return NULL;
}