update (bddd6d5e) · Commits · 郑智淋 / lammps

cmake/CMakeLists.txt

+1 −3

Original line number	Diff line number	Diff line
		@@ -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)

doc/utils/sphinx-config/false_positives.txt

+2 −0

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

src/USER-MESONT/pair_mesont_tpm.cpp

+13 −0

Original line number	Diff line number	Diff line
		@@ -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;

src/atom.cpp

+39 −20

Original line number	Diff line number	Diff line
		@@ -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;
		}

src/atom.h

+9 −6

Original line number	Diff line number	Diff line
		@@ -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;

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