ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

update

Browse Source
This commit is contained in:
iafoss
2020-05-19 23:19:49 -04:00
parent ed43c1e22b
commit bddd6d5e84
8 changed files with 67 additions and 31 deletions
Download Patch File Download Diff File Expand all files Collapse all files

4
cmake/CMakeLists.txt
View File

@ -429,8 +429,7 @@ if(PKG_USER-MESONT)
add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES})
list(APPEND LAMMPS_LINK_LIBS ${PKG_LIB})
target_include_directories(${PKG_LIB} PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB})
#include(Packages/USER-MESONT)
#list(APPEND DEFAULT_PACKAGES "USER-MESONT")
set(USER-MESONT_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-MESONT)
file(GLOB USER-MESONT_SOURCES ${USER-MESONT_SOURCES_DIR}/[^.]*.cpp)
file(GLOB USER-MESONT_HEADERS ${USER-MESONT_SOURCES_DIR}/[^.]*.h)
@ -438,7 +437,6 @@ if(PKG_USER-MESONT)
RegisterStyles(${USER-MESONT_SOURCES_DIR})
list(APPEND LIB_SOURCES ${USER-MESONT_SOURCES})
include_directories(${USER-MESONT_SOURCES_DIR})
endif()
if(PKG_USER-AWPMD)

2
doc/utils/sphinx-config/false_positives.txt
View File

@ -840,6 +840,7 @@ Espanol
Eshelby
eshelby
eskm
esph
estretch
esu
esub
@ -2647,6 +2648,7 @@ Schulten
Schunk
Schuring
Schwen
screenshot
screenshots
Scripta
sdk

13
src/USER-MESONT/pair_mesont_tpm.cpp
View File

@ -413,6 +413,19 @@ void PairMESONTTPM::compute(int eflag, int vflag){
X1, X2, X3, R123, L123, BBF2);
}
//share new values of buckling
if (BendingMode == 1){
for (int i = 0; i < nall; i++){
int idx = ntlist.get_idx(i);
buckling[idx] = b_sort[i];
}
comm->forward_comm_pair(this);
for (int i = 0; i < nall; i++){
int idx = ntlist.get_idx(i);
b_sort[i] = buckling[idx];
}
}
//segment-segment and segment-tube interactions
int n_segments = ntlist.get_segments().size();
double Rmax = 0.0;

59
src/atom.cpp
View File

@ -93,6 +93,10 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
ellipsoid = line = tri = body = NULL;
// molecular systems
molecule = NULL;
molindex = molatom = NULL;
bond_per_atom = extra_bond_per_atom = 0;
num_bond = NULL;
bond_type = NULL;
@ -146,7 +150,6 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
// USER-MESONT package
mesont_flag = 0;
length = NULL;
buckling = NULL;
bond_nt = NULL;
@ -299,6 +302,11 @@ Atom::~Atom()
memory->destroy(cv);
memory->destroy(vest);
// USER-MESONT package
memory->destroy(length);
memory->destroy(buckling);
memory->destroy(bond_nt);
memory->destroy(contact_radius);
memory->destroy(smd_data_9);
memory->destroy(smd_stress);
@ -373,12 +381,6 @@ Atom::~Atom()
for (int i = 0; i < nmolecule; i++) delete molecules[i];
memory->sfree(molecules);
// USER-MESONT package
memory->destroy(length);
memory->destroy(buckling);
memory->destroy(bond_nt);
// delete per-type arrays
delete [] mass;
@ -554,6 +556,12 @@ void Atom::peratom_create()
add_peratom("cc",&cc,DOUBLE,1);
add_peratom("cc_flux",&cc_flux,DOUBLE,1,1); // set per-thread flag
// USER-MESONT package
add_peratom("length",&length,DOUBLE,0);
add_peratom("buckling",&buckling,INT,0);
add_peratom("bond_nt",&bond_nt,tagintsize,2);
// USER-SPH package
add_peratom("rho",&rho,DOUBLE,0);
@ -679,6 +687,7 @@ void Atom::set_atomflag_defaults()
sp_flag = 0;
x0_flag = 0;
smd_flag = damage_flag = 0;
mesont_flag = 0;
contact_radius_flag = smd_data_9_flag = smd_stress_flag = 0;
eff_plastic_strain_flag = eff_plastic_strain_rate_flag = 0;
@ -1236,16 +1245,23 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
error->all(FLERR,"Incorrect atom format in data file");
}
if (imageflag)
imagedata = ((imageint) (atoi(values[iptr]) + IMGMAX) & IMGMASK) |
(((imageint) (atoi(values[iptr+1]) + IMGMAX) & IMGMASK) << IMGBITS) |
(((imageint) (atoi(values[iptr+2]) + IMGMAX) & IMGMASK) << IMG2BITS);
else imagedata = ((imageint) IMGMAX << IMG2BITS) |
((imageint) IMGMAX << IMGBITS) | IMGMAX;
int imx = 0;
int imy = 0;
int imz = 0;
if (imageflag) {
imx = utils::inumeric(FLERR,values[iptr],false,lmp);
imy = utils::inumeric(FLERR,values[iptr+1],false,lmp);
imz = utils::inumeric(FLERR,values[iptr+2],false,lmp);
if ((domain->dimension == 2) && (imz != 0))
error->all(FLERR,"Z-direction image flag must be 0 for 2d-systems");
}
imagedata = ((imageint) (imx + IMGMAX) & IMGMASK) |
(((imageint) (imy + IMGMAX) & IMGMASK) << IMGBITS) |
(((imageint) (imz + IMGMAX) & IMGMASK) << IMG2BITS);
xdata[0] = atof(values[xptr]);
xdata[1] = atof(values[xptr+1]);
xdata[2] = atof(values[xptr+2]);
xdata[0] = utils::numeric(FLERR,values[xptr],false,lmp);
xdata[1] = utils::numeric(FLERR,values[xptr+1],false,lmp);
xdata[2] = utils::numeric(FLERR,values[xptr+2],false,lmp);
if (shiftflag) {
xdata[0] += shift[0];
xdata[1] += shift[1];
@ -2539,6 +2555,11 @@ void *Atom::extract(char *name)
if (strcmp(name,"cv") == 0) return (void *) cv;
if (strcmp(name,"vest") == 0) return (void *) vest;
// USER-MESONT package
if (strcmp(name,"length") == 0) return (void *) length;
if (strcmp(name,"buckling") == 0) return (void *) buckling;
if (strcmp(name,"bond_nt") == 0) return (void *) bond_nt;
if (strcmp(name, "contact_radius") == 0) return (void *) contact_radius;
if (strcmp(name, "smd_data_9") == 0) return (void *) smd_data_9;
if (strcmp(name, "smd_stress") == 0) return (void *) smd_stress;
@ -2551,10 +2572,8 @@ void *Atom::extract(char *name)
if (strcmp(name,"dpdTheta") == 0) return (void *) dpdTheta;
if (strcmp(name,"edpd_temp") == 0) return (void *) edpd_temp;
// USER-MESONT package
if (strcmp(name,"length") == 0) return (void *) length;
if (strcmp(name,"buckling") == 0) return (void *) buckling;
if (strcmp(name,"bond_nt") == 0) return (void *) bond_nt;
// end of customization section
// --------------------------------------------------------------------
return NULL;
}

15
src/atom.h
View File

@ -127,12 +127,6 @@ class Atom : protected Pointers {
double *vest_temp;
double *edpd_cv; // heat capacity
int cc_species;
double *contact_radius;
double **smd_data_9;
double **smd_stress;
double *eff_plastic_strain;
double *eff_plastic_strain_rate;
double *damage;
// USER-MESONT package
@ -140,6 +134,15 @@ class Atom : protected Pointers {
int *buckling;
tagint **bond_nt;
// USER-SMD package
double *contact_radius;
double **smd_data_9;
double **smd_stress;
double *eff_plastic_strain;
double *eff_plastic_strain_rate;
double *damage;
// USER-SPH package
double *rho,*drho,*esph,*desph,*cv;

1
src/compute_property_atom.cpp
View File

@ -376,6 +376,7 @@ ComputePropertyAtom::ComputePropertyAtom(LAMMPS *lmp, int narg, char **arg) :
"vector does not exist");
pack_choice[i] = &ComputePropertyAtom::pack_dname;
}
else if (strcmp(arg[iarg],"buckling") == 0) {
if (!atom->mesont_flag)
error->all(FLERR,"Compute property/atom for "