/dports/science/liggghts/LIGGGHTS-PUBLIC-3.8.0-26-g6e873439/src/ |
H A D | math_extra_liggghts_superquadric.cpp | 637 …double sine = (fabs(LAMMPS_NS::vectorDot3D(v,v) / (LAMMPS_NS::vectorDot3D(gradA, gradA) * LAMMPS_N… in calc_F() 653 double mu_sq = -LAMMPS_NS::vectorDot3D(gradA,gradB) / LAMMPS_NS::vectorDot3D(gradB,gradB); in calc_F() 662 …double sine = (fabs(LAMMPS_NS::vectorDot3D(v,v) / (LAMMPS_NS::vectorDot3D(gradA, gradA) * LAMMPS_N… in calc_F() 687 …double sin_ = sqrt(fabs(LAMMPS_NS::vectorDot3D(v,v) / (LAMMPS_NS::vectorDot3D(gradA, gradA) * LAMM… in calc_F_new() 710 …double sin_ = sqrt(fabs(LAMMPS_NS::vectorDot3D(v,v) / (LAMMPS_NS::vectorDot3D(gradA, gradA) * LAMM… in calc_F_new() 1052 …double sin2A = fabs(LAMMPS_NS::vectorDot3D(vA,vA)) / (LAMMPS_NS::vectorDot3D(gradA, gradA) * (LAMM… in calc_F_IP() 1053 …double sin2B = fabs(LAMMPS_NS::vectorDot3D(vB,vB)) / (LAMMPS_NS::vectorDot3D(gradB, gradB) * (LAMM… in calc_F_IP() 1096 …double sin2A = fabs(LAMMPS_NS::vectorDot3D(vA,vA)) / (LAMMPS_NS::vectorDot3D(gradA, gradA) * (LAMM… in calc_F_IP() 1097 …double sin2B = fabs(LAMMPS_NS::vectorDot3D(vB,vB)) / (LAMMPS_NS::vectorDot3D(gradB, gradB) * (LAMM… in calc_F_IP() 1495 LAMMPS_NS::vectorNegate3D(en); in extended_overlap_algorithm() [all …]
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H A D | region_neighbor_list_definitions.h | 54 namespace LAMMPS_NS { 86 LAMMPS_NS::vectorCopy3D(_pos, x); in Particle() 100 LAMMPS_NS::vectorCopy3D(pos, x); in Particle() 102 LAMMPS_NS::vectorCopy4D(quaternion_, quaternion); in Particle() 103 LAMMPS_NS::vectorCopy3D(shape_, shape); in Particle() 104 LAMMPS_NS::vectorCopy2D(blockiness_, blockiness); in Particle() 120 LAMMPS_NS::vectorCopy3D(_pos, x); 138 LAMMPS_NS::vectorCopy3D(pos, x); 140 LAMMPS_NS::vectorCopy4D(quaternion_, quaternion); 141 LAMMPS_NS::vectorCopy3D(shape_, shape); [all …]
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H A D | math_extra_liggghts_nonspherical.cpp | 124 return LAMMPS_NS::vectorMag3D(delta); in point_line_distance() 130 double omega_mag = LAMMPS_NS::vectorMag3D(omega); in integrate_quat() 146 LAMMPS_NS::vectorCopy4D(quat_temp, quat); in integrate_quat() 238 LAMMPS_NS::vectorSubtract3D(Q1, P1, d1); in line_segments_distance() 239 LAMMPS_NS::vectorSubtract3D(Q2, P2, d2); in line_segments_distance() 240 LAMMPS_NS::vectorSubtract3D(P1, P2, r); in line_segments_distance() 244 const double f = LAMMPS_NS::vectorDot3D(d2, r); in line_segments_distance() 250 LAMMPS_NS::vectorCopy3D(P1, C1); in line_segments_distance() 251 LAMMPS_NS::vectorCopy3D(P2, C2); in line_segments_distance() 258 const double c = LAMMPS_NS::vectorDot3D(d1, r); in line_segments_distance() [all …]
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H A D | fix_nve_asphere_base.cpp | 114 if(LAMMPS_NS::vectorMag3D(wbody)*dt > 1.0) in integrate_dynamic_euler() 357 if(std::isnan(LAMMPS_NS::vectorMag3D(x[i]))) in initial_integrate() 359 if(std::isnan(LAMMPS_NS::vectorMag3D(v[i]))) in initial_integrate() 361 if(std::isnan(LAMMPS_NS::vectorMag3D(f[i]))) in initial_integrate() 363 if(std::isnan(LAMMPS_NS::vectorMag4D(quat[i]))) in initial_integrate() 386 if(std::isnan(LAMMPS_NS::vectorMag3D(v[i]))) in initial_integrate() 394 if(std::isnan(LAMMPS_NS::vectorMag3D(x[i]))) in initial_integrate() 503 if(std::isnan(LAMMPS_NS::vectorMag4D(quat[i]))) in initial_integrate() 555 if(std::isnan(LAMMPS_NS::vectorMag3D(v[i]))) in final_integrate() 557 if(std::isnan(LAMMPS_NS::vectorMag3D(f[i]))) in final_integrate() [all …]
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H A D | superquadric.cpp | 640 double F_mag = LAMMPS_NS::vectorMag3D(F); in calc_curvature_coefficient() 828 return LAMMPS_NS::vectorMag4D(F); in calc_F() 854 LAMMPS_NS::vectorSubtract3D(p, p0, n); in point_surface_projection() 856 …double sine = sqrt(fabs(LAMMPS_NS::vectorDot3D(v,v) / (LAMMPS_NS::vectorDot3D(grad_local, grad_loc… in point_surface_projection() 858 double l = LAMMPS_NS::vectorDot3D(grad_local, n) / LAMMPS_NS::vectorDot3D(grad_local, grad_local); in point_surface_projection() 896 LAMMPS_NS::vectorCopy3D(p_new, p); in point_surface_projection() 922 LAMMPS_NS::vectorCopy4D(Fa, F); in point_surface_projection() 927 LAMMPS_NS::vectorCopy4D(Fb, F); in point_surface_projection() 942 LAMMPS_NS::vectorSubtract3D(p, p0, n); in point_surface_projection() 945 …sine = sqrt(fabs(LAMMPS_NS::vectorDot3D(v,v) / (LAMMPS_NS::vectorDot3D(grad_local, grad_local) * L… in point_surface_projection() [all …]
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H A D | math_extra_liggghts.h | 362 LAMMPS_NS::vectorCopy3D(ex_local,M[0]); in cartesian_coosys_to_local() 363 LAMMPS_NS::vectorCopy3D(ey_local,M[1]); in cartesian_coosys_to_local() 364 LAMMPS_NS::vectorCopy3D(ez_local,M[2]); in cartesian_coosys_to_local() 379 double dot1 = LAMMPS_NS::vectorDot3D(ex_local,ey_local); in cartesian_coosys_to_local_orthogonal() 380 double dot2 = LAMMPS_NS::vectorDot3D(ey_local,ez_local); in cartesian_coosys_to_local_orthogonal() 469 LAMMPS_NS::vectorCopy3D(result,vec); in vec_quat_rotate() 562 double a = LAMMPS_NS::vectorDot3D(ap,edgeVec[0]); in calcBaryTriCoords() 563 double b = LAMMPS_NS::vectorDot3D(ap,edgeVec[2]); in calcBaryTriCoords() 577 double a = LAMMPS_NS::vectorDot3D(ap,edgeVec0); in calcBaryTriCoords() 578 double b = LAMMPS_NS::vectorDot3D(ap,edgeVec2); in calcBaryTriCoords() [all …]
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H A D | probability_distribution.h | 58 PDF(LAMMPS_NS::Error *error) in PDF() 74 LAMMPS_NS::Error *error; 114 template <int RAND_STYLE> inline double rand_value(PDF *pdf,LAMMPS_NS::RanPark *rp) in rand_value() 143 template<> inline double rand_value<RANDOM_CONSTANT>(PDF *pdf,LAMMPS_NS::RanPark *rp) 173 template<> inline double rand_value<RANDOM_UNIFORM>(PDF *pdf,LAMMPS_NS::RanPark *rp) 206 template<> inline double rand_value<RANDOM_GAUSSIAN>(PDF *pdf,LAMMPS_NS::RanPark *rp) 247 template<> inline double rand_value<RANDOM_LOGNORMAL>(PDF *pdf,LAMMPS_NS::RanPark *rp) 281 inline double rand(PDF *pdf,LAMMPS_NS::RanPark *rp) in rand()
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H A D | math_extra_liggghts_nonspherical.h | 439 double norm_sq_inv = 1.0 / LAMMPS_NS::vectorMag4D(quat); in invquat() 544 LAMMPS_NS::vectorCross3D(sidata.omega_i, xci, v_rot_i); in surfacesIntersectNonSpherical() 545 LAMMPS_NS::vectorCopy3D(v_rot_i, v_rot_relative); in surfacesIntersectNonSpherical() 546 LAMMPS_NS::vectorCopy3D(sidata.omega_i, omega_relative); in surfacesIntersectNonSpherical() 547 sidata.cri = LAMMPS_NS::vectorMag3D(xci); in surfacesIntersectNonSpherical() 551 LAMMPS_NS::vectorCross3D(sidata.omega_i, xci, v_rot_i); in surfacesIntersectNonSpherical() 552 LAMMPS_NS::vectorCross3D(sidata.omega_j, xcj, v_rot_j); in surfacesIntersectNonSpherical() 553 LAMMPS_NS::vectorSubtract3D(v_rot_i, v_rot_j, v_rot_relative); in surfacesIntersectNonSpherical() 555 sidata.cri = LAMMPS_NS::vectorMag3D(xci); in surfacesIntersectNonSpherical() 556 sidata.crj = LAMMPS_NS::vectorMag3D(xcj); in surfacesIntersectNonSpherical() [all …]
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H A D | math_extra_liggghts_superquadric.h | 65 …initial_point1, double *result_point, double &fi, double &fj, bool *fail, LAMMPS_NS::Error *error); 70 double *contact_point, double &fi, double &fj,LAMMPS_NS::Error *error); 72 …, double *prev_step_point, double *contact_point, double &fi, double &fj, LAMMPS_NS::Error *error); 83 …uperquadric *particle_i, Superquadric *particle_j, double *initial_guess, LAMMPS_NS::Error *error);
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H A D | fix_template_sphere.h | 126 LAMMPS_NS::FixPropertyAtom* get_fix_property(const int i) const 132 void init_fix_properties(std::vector<std::pair<LAMMPS_NS::FixPropertyAtom*, int> > &fpa_list) 134 std::vector<std::pair<LAMMPS_NS::FixPropertyAtom*, int> >::iterator it = fpa_list.begin(); 164 std::vector<LAMMPS_NS::FixPropertyAtom*> fix_properties; 170 namespace LAMMPS_NS {
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H A D | region_neighbor_list.h | 68 namespace LAMMPS_NS { 87 RegionNeighborList(LAMMPS_NS::LAMMPS *lmp); 108 …virtual bool setBoundingBox(LAMMPS_NS::BoundingBox & bb, double maxrad, bool extend = true, bool f… 123 std::vector<LAMMPS_NS::Bin<INTERPOLATE> > getBins() const in getBins()
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/dports/science/lammps/lammps-stable_29Sep2021/unittest/c-library/ |
H A D | test_library_open.cpp | 28 LAMMPS_NS::LAMMPS *lmp = (LAMMPS_NS::LAMMPS *)handle; in TEST() 56 LAMMPS_NS::LAMMPS *lmp = (LAMMPS_NS::LAMMPS *)handle; in TEST() 80 if (!LAMMPS_NS::LAMMPS::is_installed_pkg("KOKKOS")) GTEST_SKIP(); in TEST() 92 LAMMPS_NS::LAMMPS *lmp = (LAMMPS_NS::LAMMPS *)handle; in TEST() 121 LAMMPS_NS::LAMMPS *lmp = (LAMMPS_NS::LAMMPS *)handle; in TEST() 140 if (!LAMMPS_NS::LAMMPS::is_installed_pkg("OPENMP")) GTEST_SKIP(); in TEST() 153 LAMMPS_NS::LAMMPS *lmp = (LAMMPS_NS::LAMMPS *)handle; in TEST() 182 LAMMPS_NS::LAMMPS *lmp = (LAMMPS_NS::LAMMPS *)handle; in TEST()
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/dports/science/lammps/lammps-stable_29Sep2021/unittest/formats/ |
H A D | test_potential_file_reader.cpp | 39 using namespace LAMMPS_NS; 47 constexpr int LAMMPS_NS::PairSW::NPARAMS_PER_LINE; 48 constexpr int LAMMPS_NS::PairComb::NPARAMS_PER_LINE; 49 constexpr int LAMMPS_NS::PairComb3::NPARAMS_PER_LINE; 50 constexpr int LAMMPS_NS::PairTersoff::NPARAMS_PER_LINE; 51 constexpr int LAMMPS_NS::PairTersoffMOD::NPARAMS_PER_LINE; 52 constexpr int LAMMPS_NS::PairTersoffMODC::NPARAMS_PER_LINE; 53 constexpr int LAMMPS_NS::PairTersoffZBL::NPARAMS_PER_LINE; 54 constexpr int LAMMPS_NS::PairGW::NPARAMS_PER_LINE; 55 constexpr int LAMMPS_NS::PairGWZBL::NPARAMS_PER_LINE; [all …]
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/dports/science/lammps/lammps-stable_29Sep2021/unittest/fortran/ |
H A D | wrap_create.cpp | 29 LAMMPS_NS::LAMMPS *lmp = (LAMMPS_NS::LAMMPS *)handle; in TEST() 48 LAMMPS_NS::LAMMPS *lmp = (LAMMPS_NS::LAMMPS *)handle; in TEST() 67 LAMMPS_NS::LAMMPS *lmp = (LAMMPS_NS::LAMMPS *)handle; in TEST() 87 LAMMPS_NS::LAMMPS *lmp = (LAMMPS_NS::LAMMPS *)handle; in TEST()
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/dports/science/lammps/lammps-stable_29Sep2021/src/REAXFF/ |
H A D | reaxff_control.cpp | 38 using LAMMPS_NS::utils::getsyserror; 39 using LAMMPS_NS::utils::sfgets; 40 using LAMMPS_NS::utils::logmesg; 41 using LAMMPS_NS::ValueTokenizer; 81 LAMMPS_NS::TextFileReader reader(control_file, "ReaxFF control"); in Read_Control_File() 119 } catch (LAMMPS_NS::EOFException &) { in Read_Control_File()
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H A D | reaxff_types.h | 30 namespace LAMMPS_NS { 44 typedef LAMMPS_NS::tagint rc_tagint; 45 typedef LAMMPS_NS::bigint rc_bigint; 204 LAMMPS_NS::Error *error_ptr; 205 LAMMPS_NS::Pair *pair_ptr; 206 LAMMPS_NS::Memory *mem_ptr; 234 LAMMPS_NS::Error *error_ptr; 235 LAMMPS_NS::LAMMPS *lmp_ptr; 364 class LAMMPS_NS::Error *error_ptr;
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/dports/science/lammps/lammps-stable_29Sep2021/lib/atc/ |
H A D | LammpsInterface.h | 19 typedef LAMMPS_NS::RanPark* RNG_POINTER; 29 typedef LAMMPS_NS::Pair* POTENTIAL; 32 namespace LAMMPS_NS { 358 LAMMPS_NS::bigint natoms() const; 593 LAMMPS_NS::bigint ntimestep() const; 673 LAMMPS_NS::Compute * const_to_active(const LAMMPS_NS::Compute* computePointer) const; 675 LAMMPS_NS::LAMMPS * lammps_; 677 LAMMPS_NS::Fix * fixPointer_; 680 mutable LAMMPS_NS::NeighList *list_; 692 mutable LAMMPS_NS::Compute * atomPE_; [all …]
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H A D | LammpsInterface.cpp | 50 using LAMMPS_NS::bigint; 51 using LAMMPS_NS::utils::read_lines_from_file; 862 LAMMPS_NS::Atom * atom = lammps_->atom; in delete_atom() 872 LAMMPS_NS::Atom * atom = lammps_->atom; in insert_atom() 891 LAMMPS_NS::Atom * atom = lammps_->atom; in reset_ghosts() 909 LAMMPS_NS::Atom * atom = lammps_->atom; in shortrange_energy() 953 LAMMPS_NS::Pair *pair = nullptr; in potential() 963 LAMMPS_NS::Atom * atom = lammps_->atom; in type_to_groupbit() 1404 set<LAMMPS_NS::Compute * >::iterator iter; in computes_addstep() 1458 LAMMPS_NS::Compute* cmpt = const_cast<LAMMPS_NS::Compute* >(computePointer); in const_to_active() [all …]
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/dports/science/liggghts/LIGGGHTS-PUBLIC-3.8.0-26-g6e873439/lib/atc/ |
H A D | LammpsInterface.h | 16 typedef LAMMPS_NS::RanPark* RNG_POINTER; 27 typedef LAMMPS_NS::Pair* POTENTIAL; 30 namespace LAMMPS_NS { 333 LAMMPS_NS::bigint natoms() const; 568 LAMMPS_NS::bigint ntimestep() const; 648 LAMMPS_NS::Compute * const_to_active(const LAMMPS_NS::Compute* computePointer) const; 650 LAMMPS_NS::LAMMPS * lammps_; 652 LAMMPS_NS::Fix * fixPointer_; 655 mutable LAMMPS_NS::NeighList *list_; 667 mutable LAMMPS_NS::Compute * atomPE_; [all …]
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H A D | LammpsInterface.cpp | 49 using LAMMPS_NS::bigint; 834 LAMMPS_NS::Atom * atom = lammps_->atom; in delete_atom() 844 LAMMPS_NS::Atom * atom = lammps_->atom; in insert_atom() 854 LAMMPS_NS::Fix **fix = lammps_->modify->fix; in insert_atom() 863 LAMMPS_NS::Atom * atom = lammps_->atom; in reset_ghosts() 881 LAMMPS_NS::Atom * atom = lammps_->atom; in shortrange_energy() 925 LAMMPS_NS::Pair *pair = NULL; in potential() 935 LAMMPS_NS::Atom * atom = lammps_->atom; in type_to_groupbit() 1376 set<LAMMPS_NS::Compute * >::iterator iter; in computes_addstep() 1430 LAMMPS_NS::Compute* cmpt = const_cast<LAMMPS_NS::Compute* >(computePointer); in const_to_active() [all …]
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/dports/science/lammps/lammps-stable_29Sep2021/doc/src/ |
H A D | Developer_utils.rst | 249 using namespace LAMMPS_NS; 281 using namespace LAMMPS_NS; 312 .. doxygenclass:: LAMMPS_NS::Tokenizer 320 .. doxygenclass:: LAMMPS_NS::ValueTokenizer 372 .. doxygenclass:: LAMMPS_NS::ArgInfo 443 .. doxygenclass:: LAMMPS_NS::TextFileReader 472 <LAMMPS_NS::MyPage::vgot>`. 478 using namespace LAMMPS_NS; 507 .. doxygenclass:: LAMMPS_NS::MyPage 511 .. doxygenclass:: LAMMPS_NS::MyPoolChunk [all …]
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H A D | Errors_debug.rst | 113 …#1 0x00000000004cf0a2 in LAMMPS_NS::Verlet::setup (this=0x7e6c90, flag=1) at /home/akohlmey/compi… 114 …#2 0x000000000049db42 in LAMMPS_NS::Run::command (this=this@entry=0x7fffffffcca0, narg=narg@entry… 116 …#3 0x000000000041258a in LAMMPS_NS::Input::command_creator<LAMMPS_NS::Run> (lmp=<optimized out>, … 119 …#5 0x00000000004111fb in LAMMPS_NS::Input::file (this=0x7d1410) at /home/akohlmey/compile/lammps/… 165 …#0 0x00000000006653ab in LAMMPS_NS::PairLJCut::compute (this=0x1b10740, eflag=1, vflag=<optimized… 222 ==1933642== at 0x6653AB: LAMMPS_NS::PairLJCut::compute(int, int) (pair_lj_cut.cpp:139) 223 ==1933642== by 0x4CF0A1: LAMMPS_NS::Verlet::setup(int) (verlet.cpp:131) 224 ==1933642== by 0x49DB41: LAMMPS_NS::Run::command(int, char**) (run.cpp:177) 225 …==1933642== by 0x412589: void LAMMPS_NS::Input::command_creator<LAMMPS_NS::Run>(LAMMPS_NS::LAMM… 226 ==1933642== by 0x410AD2: LAMMPS_NS::Input::execute_command() (input.cpp:864) [all …]
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H A D | Cplusplus.rst | 19 instance of the :cpp:class:`LAMMPS_NS::LAMMPS` class. In C++ this can 35 LAMMPS_NS::LAMMPS *lmp; 44 lmp = new LAMMPS_NS::LAMMPS(lmpargc, (char **)lmpargv, MPI_COMM_WORLD); 66 :cpp:class:`Input <LAMMPS_NS::Input>` class an instance of which is a 67 member of the :cpp:class:`LAMMPS <LAMMPS_NS::LAMMPS>` class. You have 77 using namespace LAMMPS_NS;
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/dports/science/lammps/lammps-stable_29Sep2021/cmake/Modules/ |
H A D | generate_lmpgitversion.cmake | 27 set(temp "${temp}const bool LAMMPS_NS::LAMMPS::has_git_info = ${temp_git_info};\n") 28 set(temp "${temp}const char LAMMPS_NS::LAMMPS::git_commit[] = \"${temp_git_commit}\";\n") 29 set(temp "${temp}const char LAMMPS_NS::LAMMPS::git_branch[] = \"${temp_git_branch}\";\n") 30 set(temp "${temp}const char LAMMPS_NS::LAMMPS::git_descriptor[] = \"${temp_git_describe}\";\n")
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/dports/science/lammps/lammps-stable_29Sep2021/src/GPU/ |
H A D | gpu_extra.h | 49 inline void check_flag(int error_flag, LAMMPS_NS::Error *error, MPI_Comm &world) in check_flag() 91 inline void gpu_ready(LAMMPS_NS::Modify *modify, LAMMPS_NS::Error *error) in gpu_ready()
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