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Merge pull request #641 from lammps/doc-tweak 

small update to docs for new commands
This commit is contained in:
Steve Plimpton 2017-09-06 08:52:51 -06:00 committed by GitHub
parent 4161868bcf d886cc91f3
commit c80203cb01
4 changed files with 95 additions and 92 deletions
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1
doc/src/Section_commands.txt
View File

@ -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,

2
doc/src/compute.txt
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@ -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

4
doc/src/fix_saed_vtk.txt
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@ -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:]

180
src/USER-MISC/fix_ttm_mod.cpp
View File

@ -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<unsigned int>(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<unsigned int>(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