Merge branch 'develop'

.gitlab-ci.yml

@@ -12,17 +12,17 @@ install:
   stage: install
   only:
     - develop
-    - develop-mat
+    - mergingPML
 
   script:
     # Force workdir cleaning in case of retried
     - echo "CI_PIPELINE_ID = " $CI_PIPELINE_ID
     - env
-    - if [ -d /sps/gitlab-runner/$CI_PIPELINE_ID ] ; then rm -rf /sps/gitlab-runner/$CI_PIPELINE_ID ; fi
+    - if [ -d /sps3/gitlab-runner/$CI_PIPELINE_ID ] ; then rm -rf /sps/gitlab-runner/$CI_PIPELINE_ID ; fi
     # Move in test dir
-    - mkdir -p /sps/gitlab-runner/$CI_PIPELINE_ID
-    - cp -r $CI_PROJECT_DIR /sps/gitlab-runner/$CI_PIPELINE_ID
-    - cd /sps/gitlab-runner/$CI_PIPELINE_ID/smilei
+    - mkdir -p /sps3/gitlab-runner/$CI_PIPELINE_ID
+    - cp -r $CI_PROJECT_DIR /sps3/gitlab-runner/$CI_PIPELINE_ID
+    - cd /sps3/gitlab-runner/$CI_PIPELINE_ID/smilei
     # Set the environment
     - make uninstall_happi
     - make happi
@@ -31,134 +31,134 @@ compile_default:
   stage: compile_default
   only:
     - develop
-    - develop-mat
+    - mergingPML
 
   script:
     # Move in test dir
-    - cd /sps/gitlab-runner/$CI_PIPELINE_ID/smilei/validation
+    - cd /sps3/gitlab-runner/$CI_PIPELINE_ID/smilei/validation
     # Run validation script
-    - python validation.py -c  -v -l "/sps/gitlab-runner/logs" -t "00:30:00"
+    - python validation.py -c  -v -l "/sps3/gitlab-runner/logs" -t "00:30:00"
 
 run1D:
   stage: run_default
   only:
     - develop
-    - develop-mat
+    - mergingPML
 
   script:
     # Move in test dir
-    - cd /sps/gitlab-runner/$CI_PIPELINE_ID/smilei/validation
+    - cd /sps3/gitlab-runner/$CI_PIPELINE_ID/smilei/validation
     # Run validation script
-    - python validation.py -b "tst1d_*_*.py" -m 2 -o 12 -v -r 1 -l "/sps/gitlab-runner/logs"
-    - python validation.py -b "tst_ionization_current_1d*.py" -m 2 -o 12 -v -r 1 -l "/sps/gitlab-runner/logs"
+    - python validation.py -b "tst1d_*_*.py" -m 2 -o 12 -v -r 1 -l "/sps3/gitlab-runner/logs"
+    - python validation.py -b "tst_ionization_current_1d*.py" -m 2 -o 12 -v -r 1 -l "/sps3/gitlab-runner/logs"
 
 run2D:
   stage: run_default
   only:
     - develop
-    - develop-mat
+    - mergingPML
 
 
   script:
     # Move in test dir
-    - cd /sps/gitlab-runner/$CI_PIPELINE_ID/smilei/validation
+    - cd /sps3/gitlab-runner/$CI_PIPELINE_ID/smilei/validation
     # Run validation script
-    - python validation.py -b "tst2d_??_*.py" -m 4 -o 4 -n 1 -v -r 1 -l "/sps/gitlab-runner/logs"
-    - python validation.py -b "tst2d_s_??_*.py" -m 4 -o 4 -n 1 -v -r 1 -l "/sps/gitlab-runner/logs"
-    - python validation.py -b "tst2d_v_??_*.py" -m 4 -o 4 -n 1 -v -r 1 -l "/sps/gitlab-runner/logs"
-    - python validation.py -b "tst_ionization_current_2d*.py" -m 4 -o 4 -n 1 -v -r 1 -l "/sps/gitlab-runner/logs"
+    - python validation.py -b "tst2d_??_*.py" -m 4 -o 4 -n 1 -v -r 1 -l "/sps3/gitlab-runner/logs"
+    - python validation.py -b "tst2d_s_??_*.py" -m 4 -o 4 -n 1 -v -r 1 -l "/sps3/gitlab-runner/logs"
+    - python validation.py -b "tst2d_v_??_*.py" -m 4 -o 4 -n 1 -v -r 1 -l "/sps3/gitlab-runner/logs"
+    - python validation.py -b "tst_ionization_current_2d*.py" -m 4 -o 4 -n 1 -v -r 1 -l "/sps3/gitlab-runner/logs"
 
 run3D:
   stage: run_default
   only:
     - develop
-    - develop-mat
+    - mergingPML
 
   script:
     # Move in test dir
-    - cd /sps/gitlab-runner/$CI_PIPELINE_ID/smilei/validation
+    - cd /sps3/gitlab-runner/$CI_PIPELINE_ID/smilei/validation
     # Run validation script
-    - python validation.py -b "tst3d_??_*.py" -m 8 -o 12   --resource-file resources.json -v -r 1 -l "/sps/gitlab-runner/logs"
-    - python validation.py -b "tst3d_s_??_*.py" -m 8 -o 12 --resource-file resources.json -v -r 1 -l "/sps/gitlab-runner/logs"
-    - python validation.py -b "tst3d_v_??_*.py" -m 8 -o 12 --resource-file resources.json -v -r 1 -l "/sps/gitlab-runner/logs"
-    - python validation.py -b "tst3d_a_??_*.py" -m 8 -o 12 --resource-file resources.json -v -r 1 -l "/sps/gitlab-runner/logs"
-    - python validation.py -b "tst_ionization_current_3d*.py" -m 4 -o 4 -n 1 -v -r 1 -l "/sps/gitlab-runner/logs"
+    - python validation.py -b "tst3d_??_*.py" -m 8 -o 12   --resource-file resources.json -v -r 1 -l "/sps3/gitlab-runner/logs"
+    - python validation.py -b "tst3d_s_??_*.py" -m 8 -o 12 --resource-file resources.json -v -r 1 -l "/sps3/gitlab-runner/logs"
+    - python validation.py -b "tst3d_v_??_*.py" -m 8 -o 12 --resource-file resources.json -v -r 1 -l "/sps3/gitlab-runner/logs"
+    - python validation.py -b "tst3d_a_??_*.py" -m 8 -o 12 --resource-file resources.json -v -r 1 -l "/sps3/gitlab-runner/logs"
+    - python validation.py -b "tst_ionization_current_3d*.py" -m 4 -o 4 -n 1 -v -r 1 -l "/sps3/gitlab-runner/logs"
 
 runAM:
   stage: run_default
   only:
     - develop
-    - develop-mat
+    - mergingPML
 
   script:
     # Move in test dir
-    - cd /sps/gitlab-runner/$CI_PIPELINE_ID/smilei/validation
+    - cd /sps3/gitlab-runner/$CI_PIPELINE_ID/smilei/validation
     # Run validation script
-    - python validation.py -b "tstAM_??_*.py" -m 8 -o 12 -v -t 00:30:00 -l "/sps/gitlab-runner/logs"
+    - python validation.py -b "tstAM_??_*.py" -m 8 -o 12 -v -t 00:30:00 -l "/sps3/gitlab-runner/logs"
 
 runCollisions:
   stage: run_default
   only:
     - develop
-    - develop-mat
+    - mergingPML
 
   script:
     # Move in test dir
-    - cd /sps/gitlab-runner/$CI_PIPELINE_ID/smilei/validation
+    - cd /sps3/gitlab-runner/$CI_PIPELINE_ID/smilei/validation
     # Run checking script
-    - python validation.py -b "tst_collisions*.py" -m 4 -o 4 -n 1 -v -r 1 -l "/sps/gitlab-runner/logs"
+    - python validation.py -b "tst_collisions*.py" -m 4 -o 4 -n 1 -v -r 1 -l "/sps3/gitlab-runner/logs"
 
 compile_picsar:
   stage: compile_picsar
   only:
     - develop
-    - develop-mat
+    - mergingPML
 
   script:
-    - cd /sps/gitlab-runner/$CI_PIPELINE_ID/smilei
+    - cd /sps3/gitlab-runner/$CI_PIPELINE_ID/smilei
     - make clean
     - python validation/validation.py -k picsar -c -v
 
 run_picsar:
   stage: run_picsar
   only:
     - develop
-    - develop-mat
+    - mergingPML
 
   script:
-    - cd /sps/gitlab-runner/$CI_PIPELINE_ID/smilei/validation
+    - cd /sps3/gitlab-runner/$CI_PIPELINE_ID/smilei/validation
     - python validation.py -k picsar -b "tstAM_picsar_04_laser_wake.py" -m 4 -o 4 -n 1 -v
 
 compile_debug:
   stage: compile_debug
   only:
     - develop
-    - develop-mat
+    - mergingPML
 
   script:
-    - cd /sps/gitlab-runner/$CI_PIPELINE_ID/smilei
+    - cd /sps3/gitlab-runner/$CI_PIPELINE_ID/smilei
     - make clean
     - python validation/validation.py -k debug -c -v
 
 compile_no_mpi_threadmultiple:
   stage: compile_no_mpi_threadmultiple
   only:
     - develop
-    - develop-mat
+    - mergingPML
 
   script:
-    - cd /sps/gitlab-runner/$CI_PIPELINE_ID/smilei
+    - cd /sps3/gitlab-runner/$CI_PIPELINE_ID/smilei
     - make clean
     - python validation/validation.py -k no_mpi_tm -c -v
 
 compile_no_openmp:
   stage: compile_no_openmp
   only:
     - develop
-    - develop-mat
+    - mergingPML
 
 
   script:
-    - cd /sps/gitlab-runner/$CI_PIPELINE_ID/smilei
+    - cd /sps3/gitlab-runner/$CI_PIPELINE_ID/smilei
     - make clean
     - python validation/validation.py -k noopenmp -c -v

benchmarks/tst2d_18_em_pml.py

@@ -0,0 +1,46 @@
+# ----------------------------------------------------------------------------------------
+# 					SIMULATION PARAMETERS FOR THE PIC-CODE SMILEI
+# ----------------------------------------------------------------------------------------
+
+import numpy as np
+
+l0 = 2.*np.pi               # laser wavelength
+t0 = l0                     # optical cycle
+Lsim = [20.*l0,20.*l0]      # length of the simulation
+Tsim = 30.*t0               # duration of the simulation
+resx = 8.                  # nb of cells in on laser wavelength
+rest = 1.1*np.sqrt(2)*resx  # time of timestep in one optical cycle 
+
+Main(
+    geometry = "2Dcartesian",
+    maxwell_solver = "Yee",
+    interpolation_order = 2 ,
+    cell_length = [l0/resx,l0/resx],
+    grid_length  = Lsim,
+    number_of_patches = [ 16, 16 ],
+    timestep = t0/rest,
+    simulation_time = Tsim,
+    EM_boundary_conditions = [
+                              ['PML','PML'],
+                              ['PML','PML'],
+                             ],
+    number_of_pml_cells             = [[10,10],[10,10]],
+    random_seed = smilei_mpi_rank
+)
+
+Antenna(
+    field='Jz',
+    time_profile = lambda t: np.sin(2.*np.pi*t/t0)*np.sin(2.*np.pi*t/(4*t0))*(1.-np.heaviside(t-2*t0, 1)),
+    space_profile=gaussian(1., xfwhm=l0, yfwhm=l0, xcenter=Main.grid_length[0]*0.5, ycenter=Main.grid_length[1]*0.5)
+)
+
+globalEvery=1.
+
+DiagScalar(
+    every=globalEvery,
+    vars=['Uelm']
+)
+
+DiagFields(
+    every = 100,
+    fields = ['Ez'])

doc/Sphinx/namelist.rst

@@ -132,7 +132,8 @@ The block ``Main`` is **mandatory** and has the following syntax::
     Boundary conditions must be set to ``"remove"`` for particles,
     ``"silver-muller"`` for longitudinal EM boundaries and
     ``"buneman"`` for transverse EM boundaries.
-    Vectorization, collisions, scalar diagnostics and
+    You can alternatively use ``"PML"`` for all boundaries.
+    Vectorization, collisions and
     order-4 interpolation are not supported yet.
 
 .. py:data:: interpolation_order
@@ -272,7 +273,7 @@ The block ``Main`` is **mandatory** and has the following syntax::
   :default: ``[["periodic"]]``
 
   The boundary conditions for the electromagnetic fields. Each boundary may have one of
-  the following conditions: ``"periodic"``, ``"silver-muller"``, ``"reflective"`` or ``"ramp??"``.
+  the following conditions: ``"periodic"``, ``"silver-muller"``, ``"reflective"``, ``"ramp??"`` or ``"PML"``.
 
   | **Syntax 1:** ``[[bc_all]]``, identical for all boundaries.
   | **Syntax 2:** ``[[bc_X], [bc_Y], ...]``, different depending on x, y or z.
@@ -294,6 +295,14 @@ The block ``Main`` is **mandatory** and has the following syntax::
     Over the first half, the fields remain untouched.
     Over the second half, all fields are progressively reduced down to zero.
 
+  * ``"PML"`` stands for Perfectly Matched Layer. It is an open boundary condition.
+    The number of cells in the layer is defined by ``"number_of_pml_cells"``.
+    It supports laser injection as in ``"silver-muller"``.
+
+  .. warning::
+
+    In the current release, in order to use PML all ``"EM_boundary_conditions"`` of the simulation must be ``"PML"``.
+
 .. py:data:: EM_boundary_conditions_k
 
   :type: list of lists of floats
@@ -311,6 +320,13 @@ The block ``Main`` is **mandatory** and has the following syntax::
   | **Syntax 1:** ``[[1,0,0]]``, identical for all boundaries.
   | **Syntax 2:** ``[[1,0,0],[-1,0,0], ...]``,  different on each boundary.
 
+.. py:data:: number_of_pml_cells
+
+  :type: list of lists of integer
+  :default: ``[[6,6],[6,6],[6,6]]``
+
+  Defines the number of cells in the ``"PML"`` layers using the same alternative syntaxes as ``"EM_boundary_conditions"``.
+
 .. py:data:: time_fields_frozen
 
   :default: 0.
@@ -2272,7 +2288,7 @@ This is done by including the block ``DiagScalar``::
 
 .. warning::
 
-  Scalars diagnostics are not yet supported in ``"AMcylindrical"`` geometry.
+  Scalars diagnostics min/max cell are not yet supported in ``"AMcylindrical"`` geometry.
 
 The full list of available scalars is given in the table below.
 

doc/Sphinx/post-processing.rst

@@ -419,9 +419,9 @@ and only one mode between those three.
 
   * ``hindex``                     : the starting index of each proc in the hilbert curve
   * ``number_of_cells``            : the number of cells in each proc
-  * ``number_of_particles``        : the number of particles in each proc (except frozen ones)
+  * ``number_of_particles``        : the total number of non-frozen macro-particles in each proc (includes all species)
   * ``number_of_frozen_particles`` : the number of frozen particles in each proc
-  * ``total_load``                 : the `load` of each proc (number of particles and cells with cell_load coefficient)
+  * ``total_load``                 : the `load` of each proc (number of macro-particles and cells weighted by cell_load coefficients)
   * ``timer_global``               : global simulation time (only available for proc 0)
   * ``timer_particles``            : time spent computing particles by each proc
   * ``timer_maxwell``              : time spent solving maxwell by each proc

doc/Sphinx/releases.rst

@@ -20,6 +20,7 @@ Get Smilei
 Changes made in the repository (not released)
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
+* ``Perfectly Matched Layers`` boundary conditions for EM fields are available. Documentation is updated and a 2D Cartesian benchmark is provided.
 * Improved performance for ARM-based processors including the Fujitsu A64FX
 * Improved performance for GNU, LLVM, arm-clang and Fujitsu compilers on all types of architectures
 * Lasers can be injected from all boundaries
@@ -75,7 +76,7 @@ Projects
 
   * More spectral solvers
   * GPU support
-  * Perfectly-matched layers
+  * Perfectly-matched layers for the envelope model
 
 ----
 

src/ElectroMagn/ElectroMagn.cpp

@@ -444,6 +444,8 @@ void ElectroMagn::boundaryConditions( int itime, double time_dual, Patch *patch,
     if( emBoundCond.size()>2 ) {
         if( emBoundCond[2]!=NULL ) { // <=> if !periodic
             emBoundCond[2]->apply( this, time_dual, patch );
+        }
+        if( emBoundCond[3]!=NULL ) { // <=> if !periodic
             emBoundCond[3]->apply( this, time_dual, patch );
         }
     }

src/ElectroMagnBC/ElectroMagnBC.cpp

@@ -41,6 +41,8 @@ ElectroMagnBC::ElectroMagnBC( Params &params, Patch *patch, unsigned int i_bound
         d[i] = params.cell_length[i];
         dt_ov_d[i] = dt / d[i];
     }
+
+    pml_solver_ = NULL;
 }
 
 // Destructor for ElectromagnBC

src/ElectroMagnBC/ElectroMagnBC.h

@@ -11,6 +11,7 @@ class Patch;
 class ElectroMagn;
 class Laser;
 class Field;
+class Solver;
 
 class ElectroMagnBC
 {
@@ -28,6 +29,19 @@ class ElectroMagnBC
 
     //! Vector for the various lasers
     std::vector<Laser *> vecLaser;
+
+    virtual Field* getExPML() { ERROR("Not using PML");return NULL;}
+    virtual Field* getEyPML() { ERROR("Not using PML");return NULL;}
+    virtual Field* getEzPML() { ERROR("Not using PML");return NULL;}
+    virtual Field* getBxPML() { ERROR("Not using PML");return NULL;}
+    virtual Field* getByPML() { ERROR("Not using PML");return NULL;}
+    virtual Field* getBzPML() { ERROR("Not using PML");return NULL;}
+    virtual Field* getDxPML() { ERROR("Not using PML");return NULL;}
+    virtual Field* getDyPML() { ERROR("Not using PML");return NULL;}
+    virtual Field* getDzPML() { ERROR("Not using PML");return NULL;}
+    virtual Field* getHxPML() { ERROR("Not using PML");return NULL;}
+    virtual Field* getHyPML() { ERROR("Not using PML");return NULL;}
+    virtual Field* getHzPML() { ERROR("Not using PML");return NULL;}
 
 protected:
 
@@ -48,6 +62,7 @@ class ElectroMagnBC
 
     //! Ratio of the time-step by the spatial-step
     std::vector<double> dt_ov_d;
+    Solver* pml_solver_;
 };
 
 #endif