diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt index 78969bc4ab..32b714e1de 100644 --- a/doc/src/Section_commands.txt +++ b/doc/src/Section_commands.txt @@ -756,6 +756,7 @@ package"_Section_accelerate.html. This is indicated by additional letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. +"aggregate/atom"_compute_cluster_atom.html, "angle"_compute_angle.html, "angle/local"_compute_angle_local.html, "angmom/chunk"_compute_angmom_chunk.html, diff --git a/doc/src/compute.txt b/doc/src/compute.txt index eed190aeb2..c06735d28e 100644 --- a/doc/src/compute.txt +++ b/doc/src/compute.txt @@ -169,6 +169,7 @@ by users which are included in the LAMMPS distribution. The list of these with links to the individual styles are given in the compute section of "this page"_Section_commands.html#cmd_5. +"aggregate/atom"_compute_cluster_atom.html - aggregate ID for each atom "angle/local"_compute_bond_local.html - theta and energy of each angle "angmom/chunk"_compute_angmom_chunk.html - angular momentum for each chunk "body/local"_compute_body_local.html - attributes of body sub-particles @@ -191,6 +192,7 @@ section of "this page"_Section_commands.html#cmd_5. "erotate/sphere"_compute_erotate_sphere.html - rotational energy of spherical particles "erotate/sphere/atom"_compute_erotate_sphere.html - rotational energy for each spherical particle "event/displace"_compute_event_displace.html - detect event on atom displacement +"fragment/atom"_compute_cluster_atom.html - fragment ID for each atom "group/group"_compute_group_group.html - energy/force between two groups of atoms "gyration"_compute_gyration.html - radius of gyration of group of atoms "gyration/chunk"_compute_gyration_chunk.html - radius of gyration for each chunk diff --git a/doc/src/fix_saed_vtk.txt b/doc/src/fix_saed_vtk.txt index 3523233cee..814e17b8e9 100644 --- a/doc/src/fix_saed_vtk.txt +++ b/doc/src/fix_saed_vtk.txt @@ -37,8 +37,8 @@ keyword = {file} or {ave} or {start} or {file} or {overwrite}:l compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5 compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo :pre -fix saed/vtk 1 1 1 c_1 file Al2O3_001.saed -fix saed/vtk 1 1 1 c_2 file Ni_000.saed :pre +fix 1 all saed/vtk 1 1 1 c_1 file Al2O3_001.saed +fix 2 all saed/vtk 1 1 1 c_2 file Ni_000.saed :pre [Description:] diff --git a/src/USER-MISC/fix_ttm_mod.cpp b/src/USER-MISC/fix_ttm_mod.cpp index 4bf90fdca3..d2fc6ac901 100644 --- a/src/USER-MISC/fix_ttm_mod.cpp +++ b/src/USER-MISC/fix_ttm_mod.cpp @@ -628,99 +628,99 @@ void FixTTMMod::end_of_step() T_electron[ixnode][iynode][iznode] = T_electron_first[ixnode][iynode][iznode]; - stability_criterion = 1.0 - - 2.0*inner_dt/el_specific_heat * + stability_criterion = 1.0 - + 2.0*inner_dt/el_specific_heat * + (el_thermal_conductivity*(1.0/dx/dx + 1.0/dy/dy + 1.0/dz/dz)); + if (stability_criterion < 0.0) { + inner_dt = 0.25*el_specific_heat / (el_thermal_conductivity*(1.0/dx/dx + 1.0/dy/dy + 1.0/dz/dz)); - if (stability_criterion < 0.0) { - inner_dt = 0.25*el_specific_heat / - (el_thermal_conductivity*(1.0/dx/dx + 1.0/dy/dy + 1.0/dz/dz)); - } - num_inner_timesteps = static_cast(update->dt/inner_dt) + 1; - inner_dt = update->dt/double(num_inner_timesteps); - if (num_inner_timesteps > 1000000) - error->warning(FLERR,"Too many inner timesteps in fix ttm/mod",0); - for (int ith_inner_timestep = 0; ith_inner_timestep < num_inner_timesteps; - ith_inner_timestep++) { - for (int ixnode = 0; ixnode < nxnodes; ixnode++) - for (int iynode = 0; iynode < nynodes; iynode++) - for (int iznode = 0; iznode < nznodes; iznode++) - T_electron_old[ixnode][iynode][iznode] = - T_electron[ixnode][iynode][iznode]; - // compute new electron T profile - duration = duration + inner_dt; - for (int ixnode = 0; ixnode < nxnodes; ixnode++) - for (int iynode = 0; iynode < nynodes; iynode++) - for (int iznode = 0; iznode < nznodes; iznode++) { - int right_xnode = ixnode + 1; - int right_ynode = iynode + 1; - int right_znode = iznode + 1; - if (right_xnode == nxnodes) right_xnode = 0; - if (right_ynode == nynodes) right_ynode = 0; - if (right_znode == nznodes) right_znode = 0; - int left_xnode = ixnode - 1; - int left_ynode = iynode - 1; - int left_znode = iznode - 1; - if (left_xnode == -1) left_xnode = nxnodes - 1; - if (left_ynode == -1) left_ynode = nynodes - 1; - if (left_znode == -1) left_znode = nznodes - 1; - double skin_layer_d = double(skin_layer); - double ixnode_d = double(ixnode); - double surface_d = double(t_surface_l); - mult_factor = 0.0; - if (duration < width){ - if (ixnode >= t_surface_l) mult_factor = (intensity/(dx*skin_layer_d))*exp((-1.0)*(ixnode_d - surface_d)/skin_layer_d); - } - if (ixnode < t_surface_l) net_energy_transfer_all[ixnode][iynode][iznode] = 0.0; - double cr_vac = 1; - if (T_electron_old[ixnode][iynode][iznode] == 0) cr_vac = 0; - double cr_v_l_x = 1; - if (T_electron_old[left_xnode][iynode][iznode] == 0) cr_v_l_x = 0; - double cr_v_r_x = 1; - if (T_electron_old[right_xnode][iynode][iznode] == 0) cr_v_r_x = 0; - double cr_v_l_y = 1; - if (T_electron_old[ixnode][left_ynode][iznode] == 0) cr_v_l_y = 0; - double cr_v_r_y = 1; - if (T_electron_old[ixnode][right_ynode][iznode] == 0) cr_v_r_y = 0; - double cr_v_l_z = 1; - if (T_electron_old[ixnode][iynode][left_znode] == 0) cr_v_l_z = 0; - double cr_v_r_z = 1; - if (T_electron_old[ixnode][iynode][right_znode] == 0) cr_v_r_z = 0; - if (cr_vac != 0) { - T_electron[ixnode][iynode][iznode] = - T_electron_old[ixnode][iynode][iznode] + - inner_dt/el_properties(T_electron_old[ixnode][iynode][iznode]).el_heat_capacity * - ((cr_v_r_x*el_properties(T_electron_old[ixnode][iynode][iznode]/2.0+T_electron_old[right_xnode][iynode][iznode]/2.0).el_thermal_conductivity* - (T_electron_old[right_xnode][iynode][iznode]-T_electron_old[ixnode][iynode][iznode])/dx - - cr_v_l_x*el_properties(T_electron_old[ixnode][iynode][iznode]/2.0+T_electron_old[left_xnode][iynode][iznode]/2.0).el_thermal_conductivity* - (T_electron_old[ixnode][iynode][iznode]-T_electron_old[left_xnode][iynode][iznode])/dx)/dx + - (cr_v_r_y*el_properties(T_electron_old[ixnode][iynode][iznode]/2.0+T_electron_old[ixnode][right_ynode][iznode]/2.0).el_thermal_conductivity* - (T_electron_old[ixnode][right_ynode][iznode]-T_electron_old[ixnode][iynode][iznode])/dy - - cr_v_l_y*el_properties(T_electron_old[ixnode][iynode][iznode]/2.0+T_electron_old[ixnode][left_ynode][iznode]/2.0).el_thermal_conductivity* - (T_electron_old[ixnode][iynode][iznode]-T_electron_old[ixnode][left_ynode][iznode])/dy)/dy + - (cr_v_r_z*el_properties(T_electron_old[ixnode][iynode][iznode]/2.0+T_electron_old[ixnode][iynode][right_znode]/2.0).el_thermal_conductivity* - (T_electron_old[ixnode][iynode][right_znode]-T_electron_old[ixnode][iynode][iznode])/dz - - cr_v_l_z*el_properties(T_electron_old[ixnode][iynode][iznode]/2.0+T_electron_old[ixnode][iynode][left_znode]/2.0).el_thermal_conductivity* - (T_electron_old[ixnode][iynode][iznode]-T_electron_old[ixnode][iynode][left_znode])/dz)/dz); - T_electron[ixnode][iynode][iznode]+=inner_dt/el_properties(T_electron[ixnode][iynode][iznode]).el_heat_capacity* - (mult_factor - - net_energy_transfer_all[ixnode][iynode][iznode]/del_vol); - } - else T_electron[ixnode][iynode][iznode] = - T_electron_old[ixnode][iynode][iznode]; - if ((T_electron[ixnode][iynode][iznode] > 0.0) && (T_electron[ixnode][iynode][iznode] < electron_temperature_min)) - T_electron[ixnode][iynode][iznode] = T_electron[ixnode][iynode][iznode] + 0.5*(electron_temperature_min - T_electron[ixnode][iynode][iznode]); - - if (el_properties(T_electron[ixnode][iynode][iznode]).el_thermal_conductivity > el_thermal_conductivity) - el_thermal_conductivity = el_properties(T_electron[ixnode][iynode][iznode]).el_thermal_conductivity; - if ((T_electron[ixnode][iynode][iznode] > 0.0) && (el_properties(T_electron[ixnode][iynode][iznode]).el_heat_capacity < el_specific_heat)) - el_specific_heat = el_properties(T_electron[ixnode][iynode][iznode]).el_heat_capacity; + } + num_inner_timesteps = static_cast(update->dt/inner_dt) + 1; + inner_dt = update->dt/double(num_inner_timesteps); + if (num_inner_timesteps > 1000000) + error->warning(FLERR,"Too many inner timesteps in fix ttm/mod",0); + for (int ith_inner_timestep = 0; ith_inner_timestep < num_inner_timesteps; + ith_inner_timestep++) { + for (int ixnode = 0; ixnode < nxnodes; ixnode++) + for (int iynode = 0; iynode < nynodes; iynode++) + for (int iznode = 0; iznode < nznodes; iznode++) + T_electron_old[ixnode][iynode][iznode] = + T_electron[ixnode][iynode][iznode]; + // compute new electron T profile + duration = duration + inner_dt; + for (int ixnode = 0; ixnode < nxnodes; ixnode++) + for (int iynode = 0; iynode < nynodes; iynode++) + for (int iznode = 0; iznode < nznodes; iznode++) { + int right_xnode = ixnode + 1; + int right_ynode = iynode + 1; + int right_znode = iznode + 1; + if (right_xnode == nxnodes) right_xnode = 0; + if (right_ynode == nynodes) right_ynode = 0; + if (right_znode == nznodes) right_znode = 0; + int left_xnode = ixnode - 1; + int left_ynode = iynode - 1; + int left_znode = iznode - 1; + if (left_xnode == -1) left_xnode = nxnodes - 1; + if (left_ynode == -1) left_ynode = nynodes - 1; + if (left_znode == -1) left_znode = nznodes - 1; + double skin_layer_d = double(skin_layer); + double ixnode_d = double(ixnode); + double surface_d = double(t_surface_l); + mult_factor = 0.0; + if (duration < width){ + if (ixnode >= t_surface_l) mult_factor = (intensity/(dx*skin_layer_d))*exp((-1.0)*(ixnode_d - surface_d)/skin_layer_d); } - } - stability_criterion = 1.0 - - 2.0*inner_dt/el_specific_heat * - (el_thermal_conductivity*(1.0/dx/dx + 1.0/dy/dy + 1.0/dz/dz)); + if (ixnode < t_surface_l) net_energy_transfer_all[ixnode][iynode][iznode] = 0.0; + double cr_vac = 1; + if (T_electron_old[ixnode][iynode][iznode] == 0) cr_vac = 0; + double cr_v_l_x = 1; + if (T_electron_old[left_xnode][iynode][iznode] == 0) cr_v_l_x = 0; + double cr_v_r_x = 1; + if (T_electron_old[right_xnode][iynode][iznode] == 0) cr_v_r_x = 0; + double cr_v_l_y = 1; + if (T_electron_old[ixnode][left_ynode][iznode] == 0) cr_v_l_y = 0; + double cr_v_r_y = 1; + if (T_electron_old[ixnode][right_ynode][iznode] == 0) cr_v_r_y = 0; + double cr_v_l_z = 1; + if (T_electron_old[ixnode][iynode][left_znode] == 0) cr_v_l_z = 0; + double cr_v_r_z = 1; + if (T_electron_old[ixnode][iynode][right_znode] == 0) cr_v_r_z = 0; + if (cr_vac != 0) { + T_electron[ixnode][iynode][iznode] = + T_electron_old[ixnode][iynode][iznode] + + inner_dt/el_properties(T_electron_old[ixnode][iynode][iznode]).el_heat_capacity * + ((cr_v_r_x*el_properties(T_electron_old[ixnode][iynode][iznode]/2.0+T_electron_old[right_xnode][iynode][iznode]/2.0).el_thermal_conductivity* + (T_electron_old[right_xnode][iynode][iznode]-T_electron_old[ixnode][iynode][iznode])/dx - + cr_v_l_x*el_properties(T_electron_old[ixnode][iynode][iznode]/2.0+T_electron_old[left_xnode][iynode][iznode]/2.0).el_thermal_conductivity* + (T_electron_old[ixnode][iynode][iznode]-T_electron_old[left_xnode][iynode][iznode])/dx)/dx + + (cr_v_r_y*el_properties(T_electron_old[ixnode][iynode][iznode]/2.0+T_electron_old[ixnode][right_ynode][iznode]/2.0).el_thermal_conductivity* + (T_electron_old[ixnode][right_ynode][iznode]-T_electron_old[ixnode][iynode][iznode])/dy - + cr_v_l_y*el_properties(T_electron_old[ixnode][iynode][iznode]/2.0+T_electron_old[ixnode][left_ynode][iznode]/2.0).el_thermal_conductivity* + (T_electron_old[ixnode][iynode][iznode]-T_electron_old[ixnode][left_ynode][iznode])/dy)/dy + + (cr_v_r_z*el_properties(T_electron_old[ixnode][iynode][iznode]/2.0+T_electron_old[ixnode][iynode][right_znode]/2.0).el_thermal_conductivity* + (T_electron_old[ixnode][iynode][right_znode]-T_electron_old[ixnode][iynode][iznode])/dz - + cr_v_l_z*el_properties(T_electron_old[ixnode][iynode][iznode]/2.0+T_electron_old[ixnode][iynode][left_znode]/2.0).el_thermal_conductivity* + (T_electron_old[ixnode][iynode][iznode]-T_electron_old[ixnode][iynode][left_znode])/dz)/dz); + T_electron[ixnode][iynode][iznode]+=inner_dt/el_properties(T_electron[ixnode][iynode][iznode]).el_heat_capacity* + (mult_factor - + net_energy_transfer_all[ixnode][iynode][iznode]/del_vol); + } + else T_electron[ixnode][iynode][iznode] = + T_electron_old[ixnode][iynode][iznode]; + if ((T_electron[ixnode][iynode][iznode] > 0.0) && (T_electron[ixnode][iynode][iznode] < electron_temperature_min)) + T_electron[ixnode][iynode][iznode] = T_electron[ixnode][iynode][iznode] + 0.5*(electron_temperature_min - T_electron[ixnode][iynode][iznode]); - } while (stability_criterion < 0.0); + if (el_properties(T_electron[ixnode][iynode][iznode]).el_thermal_conductivity > el_thermal_conductivity) + el_thermal_conductivity = el_properties(T_electron[ixnode][iynode][iznode]).el_thermal_conductivity; + if ((T_electron[ixnode][iynode][iznode] > 0.0) && (el_properties(T_electron[ixnode][iynode][iznode]).el_heat_capacity < el_specific_heat)) + el_specific_heat = el_properties(T_electron[ixnode][iynode][iznode]).el_heat_capacity; + } + } + stability_criterion = 1.0 - + 2.0*inner_dt/el_specific_heat * + (el_thermal_conductivity*(1.0/dx/dx + 1.0/dy/dy + 1.0/dz/dz)); + + } while (stability_criterion < 0.0); // output nodal temperatures for current timestep if ((nfileevery) && !(update->ntimestep % nfileevery)) { // compute atomic Ta for each grid point