change names

doc/gpumd/input_parameters/dump_piston.rst → doc/gpumd/input_parameters/dump_shock_nemd.rst

@@ -1,24 +1,23 @@
-.. _kw_dump_piston:
+.. _kw_dump_shock_nemd:
 .. index::
- single: dump_piston (keyword in run.in)
+ single: dump_shock_nemd (keyword in run.in)
 
-:attr:`dump_piston`
+:attr:`dump_shock_nemd`
 =====================
 
 In shock wave piston simulations, it's often crucial to compute thermo information at different regions, both before and after the shock wave passage.
 
-Piston simulations commonly involve millions of atoms. Dumping all the virial and velocity data for each atom can lead to excessively large output files, making data processing cumbersome. The `dump_piston` command addresses this by calculating spatial thermo information during the simulation.
+Piston simulations commonly involve millions of atoms. Dumping all the virial and velocity data for each atom can lead to excessively large output files, making data processing cumbersome. The `dump_shock_nemd` command addresses this by calculating spatial thermo information during the simulation.
 
-This feature calculates the spatial distribution of partical velocity (km/h), stress (GPa), temperature and density (g/cm3).
+This feature calculates the spatial distribution of partical velocity (km/h), stress (GPa), temperature and density (g/cm3) in *x*-direction.
 
 Syntax
 ------
 
 .. code::
 
- dump_piston direction <direction> interval <time_interval> bin_size <size of each bin>
+ dump_shock_nemd interval <time_interval> bin_size <size of each bin>
 
-- The :attr:`direction` parameter specifies the shock wave direction (x, y, or z).
 - The :attr:`interval` parameter sets the output interval (number of steps).
 - The :attr:`bin_size` parameter, optional with a default value of 10, defines the thickness of each histogram bin, measured in Angstroms.
 
@@ -29,4 +28,4 @@ To output spatial thermo information every 1000 steps for a run in the x-directi
 
 .. code::
 
- dump_piston direction x interval 1000 bin_size 20
+ dump_shock_nemd interval 1000 bin_size 20

doc/gpumd/input_parameters/ensemble_shock_nemd.rst

@@ -4,20 +4,19 @@
 =========================
 
 In a typical NEMD shock simulation, a shock wave is generated by a moving *wall*.
-We can simulate the *wall* in multiple ways:
+The *wall* can be simulated in multiple ways:
 
 - :attr:`wall_piston`: A fixed layer of atoms.
 - :attr:`wall_mirror`: A momentum mirror that reflects atoms.
 - :attr:`wall_harmonic`: A harmonic potential that pushes atoms away. It is softer than a momentum mirror.
 
-Any of these methods can generate a shock wave. There are other possible methods, but the above methods are usually enough.
+Any of these methods can generate a shock wave. While there are other possible methods, the above methods are usually sufficient.
 
+Please note that the shock wave propagates in the *x*-direction.
+Another wall is placed on the opposite side of the cell to prevent atoms from escaping.
+It is important **NOT** to use non-periodic boundary conditions in the *x*-direction, as GPUMD currently does not handle it well. A vacuum layer is automatically added on the other side of the cell.
 
-Note that the shock wave is in x direction.
-Another wall is placed at the other side of the cell to prevent atoms from escaping.
-You **MUST NOT** use non-peridic boundary condition in x dirction, since currently GPUMD can not handle it well. A vacuum layer is automatically added to the other side of the cell.
-
-We recommand to use it with the :ref:`dump_piston keyword <kw_dump_piston>`.
+It is recommended to use this with the :ref:`dump_shock_nemd keyword <kw_dump_shock_nemd>` to get the spatial distribution of thermo information.
 
 Syntax
 ------
@@ -29,7 +28,7 @@ The parameters are specified as follows:
  ensemble wall_piston vp <vp> thickness <thickness>
 
 - :attr:`<vp>`: Indicates the velocity of the moving piston in km/s.
-- :attr:`<thickness>`: Defines the thickness of the wall in Angstroms. This keyword is optional with the default value 20.
+- :attr:`<thickness>`: Defines the thickness of the wall in Angstroms. This keyword is optional with the default value of 20.
 
 .. code-block:: rst
 
@@ -42,5 +41,4 @@ The parameters are specified as follows:
  ensemble wall_harmonic vp <vp> k <k>
 
 - :attr:`<vp>`: Indicates the velocity of the moving piston in km/s.
-- :attr:`<k>`: Defines the strength of the harmonic wall in eV/A^2. This keyword is optional with the default value 10.
-
+- :attr:`<k>`: Defines the strength of the harmonic wall in eV/A^2. This keyword is optional with the default value of 10.

doc/gpumd/input_parameters/index.rst

@@ -75,4 +75,4 @@ Below you can find a listing of keywords for the ``run.in`` input file.
  dump_restart
  dump_thermo
  dump_velocity
- dump_piston
+ dump_shock_nemd

src/main_gpumd/run.cu

@@ -421,8 +421,8 @@ void Run::parse_one_keyword(std::vector<std::string>& tokens)
  measure.dump_beads.parse(param, num_param);
  } else if (strcmp(param[0], "dump_observer") == 0) {
  measure.dump_observer.parse(param, num_param);
- } else if (strcmp(param[0], "dump_piston") == 0) {
- measure.dump_piston.parse(param, num_param);
+ } else if (strcmp(param[0], "dump_shock_nemd") == 0) {
+ measure.dump_shock_nemd.parse(param, num_param);
  } else if (strcmp(param[0], "dump_dipole") == 0) {
  measure.dump_dipole.parse(param, num_param);
  } else if (strcmp(param[0], "dump_polarizability") == 0) {

src/measure/dump_piston.cu → src/measure/dump_shock_nemd.cu

@@ -13,7 +13,7 @@
  along with GPUMD. If not, see <http:https://www.gnu.org/licenses/>.
 */
 
-#include "dump_piston.cuh"
+#include "dump_shock_nemd.cuh"
 #include <cstring>
 
 namespace
@@ -139,24 +139,14 @@ void write_to_file(FILE* file, double* array, int n)
 
 } // namespace
 
-void Dump_Piston::parse(const char** param, int num_param)
+void Dump_Shock_NEMD::parse(const char** param, int num_param)
 {
  dump_ = true;
 
  printf("Dump spatial histogram thermo information for piston shock wave simulation, ");
  int i = 1;
  while (i < num_param) {
- if (strcmp(param[i], "direction") == 0) {
- if (strcmp(param[i + 1], "x") == 0)
- direction = 0;
- else if (strcmp(param[i + 1], "y") == 0)
- direction = 1;
- else if (strcmp(param[i + 1], "z") == 0)
- direction = 2;
- else
- PRINT_INPUT_ERROR("Direction should be x or y or z.");
- i += 2;
- } else if (strcmp(param[i], "interval") == 0) {
+ if (strcmp(param[i], "interval") == 0) {
  if (!is_valid_int(param[i + 1], &dump_interval_))
  PRINT_INPUT_ERROR("Dump interval should be an integer.");
  i += 2;
@@ -168,19 +158,9 @@ void Dump_Piston::parse(const char** param, int num_param)
  PRINT_INPUT_ERROR("Unknown keyword.");
  }
  }
-
- if (strcmp(param[2], "x") == 0) {
- direction = 0;
- } else if (strcmp(param[2], "y") == 0) {
- direction = 1;
- } else if (strcmp(param[2], "z") == 0) {
- direction = 2;
- } else
- PRINT_INPUT_ERROR("Direction should be x or y or z.");
- printf("in %d direction.\n", direction);
 }
 
-void Dump_Piston::preprocess(Atom& atom, Box& box)
+void Dump_Shock_NEMD::preprocess(Atom& atom, Box& box)
 {
  if (!dump_)
  return;
@@ -199,12 +179,10 @@ void Dump_Piston::preprocess(Atom& atom, Box& box)
  pyy_file = my_fopen("pyy_hist.txt", "w");
  pzz_file = my_fopen("pzz_hist.txt", "w");
  density_file = my_fopen("density_hist.txt", "w");
- com_vx_file = my_fopen("com_vx_hist.txt", "w");
- com_vy_file = my_fopen("com_vy_hist.txt", "w");
- com_vz_file = my_fopen("com_vz_hist.txt", "w");
+ com_vx_file = my_fopen("vp_hist.txt", "w");
 }
 
-void Dump_Piston::process(Atom& atom, Box& box, const int step)
+void Dump_Shock_NEMD::process(Atom& atom, Box& box, const int step)
 {
  if (!dump_ || step % dump_interval_ != 0)
  return;
@@ -295,11 +273,9 @@ void Dump_Piston::process(Atom& atom, Box& box, const int step)
  write_to_file(pzz_file, cpu_pzz.data(), bins);
  write_to_file(density_file, cpu_density.data(), bins);
  write_to_file(com_vx_file, cpu_com_vx.data(), bins);
- write_to_file(com_vy_file, cpu_com_vy.data(), bins);
- write_to_file(com_vz_file, cpu_com_vz.data(), bins);
 }
 
-void Dump_Piston::postprocess()
+void Dump_Shock_NEMD::postprocess()
 {
  if (!dump_)
  return;
@@ -310,7 +286,5 @@ void Dump_Piston::postprocess()
  fclose(pzz_file);
  fclose(density_file);
  fclose(com_vx_file);
- fclose(com_vy_file);
- fclose(com_vz_file);
  dump_ = false;
 }

src/measure/dump_piston.cuh → src/measure/dump_shock_nemd.cuh

@@ -24,7 +24,7 @@
 #include <string>
 #include <vector>
 
-class Dump_Piston
+class Dump_Shock_NEMD
 {
 public:
  void parse(const char** param, int num_param);
@@ -36,12 +36,11 @@ private:
  bool dump_ = false;
  int n;
  int dump_interval_ = -1;
- int direction;
+ int direction = 0;
  int bins;
  double slice_vol = 1;
  double avg_window = 10;
- FILE *temp_file, *pxx_file, *pyy_file, *pzz_file, *density_file, *com_vx_file, *com_vy_file,
- *com_vz_file;
+ FILE *temp_file, *pxx_file, *pyy_file, *pzz_file, *density_file, *com_vx_file;
  GPU_Vector<double> gpu_temp, gpu_pxx, gpu_pyy, gpu_pzz, gpu_density, gpu_com_vx, gpu_com_vy,
  gpu_com_vz, gpu_number;
  std::vector<double> cpu_temp, cpu_pxx, cpu_pyy, cpu_pzz, cpu_density, cpu_com_vx, cpu_com_vy,

src/measure/measure.cu

@@ -55,7 +55,7 @@ void Measure::initialize(
  dump_exyz.preprocess(number_of_atoms);
  dump_beads.preprocess(number_of_atoms, atom.number_of_beads);
  dump_observer.preprocess(number_of_atoms, number_of_potentials, force);
- dump_piston.preprocess(atom, box);
+ dump_shock_nemd.preprocess(atom, box);
  dump_dipole.preprocess(number_of_atoms, number_of_potentials, force);
  dump_polarizability.preprocess(number_of_atoms, number_of_potentials, force);
  active.preprocess(number_of_atoms, number_of_potentials, force);
@@ -85,7 +85,7 @@ void Measure::finalize(
  dump_exyz.postprocess();
  dump_beads.postprocess();
  dump_observer.postprocess();
- dump_piston.postprocess();
+ dump_shock_nemd.postprocess();
  dump_dipole.postprocess();
  dump_polarizability.postprocess();
  active.postprocess();
@@ -204,7 +204,7 @@ void Measure::process(
  step, temperature, box.get_volume(), hnemd.fe, atom.velocity_per_atom, atom.virial_per_atom);
 
  lsqt.process(atom, box, step);
- dump_piston.process(atom, box, step);
+ dump_shock_nemd.process(atom, box, step);
 
 #ifdef USE_NETCDF
  dump_netcdf.process(

src/measure/measure.cuh

@@ -22,10 +22,10 @@
 #include "dump_exyz.cuh"
 #include "dump_force.cuh"
 #include "dump_observer.cuh"
-#include "dump_piston.cuh"
 #include "dump_polarizability.cuh"
 #include "dump_position.cuh"
 #include "dump_restart.cuh"
+#include "dump_shock_nemd.cuh"
 #include "dump_thermo.cuh"
 #include "dump_velocity.cuh"
 #include "force/force.cuh"
@@ -109,7 +109,7 @@ public:
  Dump_EXYZ dump_exyz;
  Dump_Beads dump_beads;
  Dump_Observer dump_observer;
- Dump_Piston dump_piston;
+ Dump_Shock_NEMD dump_shock_nemd;
  Dump_Dipole dump_dipole;
  Dump_Polarizability dump_polarizability;
  Active active;