Merge branch 'atcollab:master' into master

Author: yysigari

.github/workflows/build-python-wheels.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-20.04, macos-12, windows-2022]
+        os: [ubuntu-22.04, macos-12, windows-2022]
 
     steps:
       - uses: actions/checkout@v4
@@ -23,12 +23,12 @@ jobs:
           fetch-depth: 0
 
       - name: Install Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: '3.9'
 
       - name: Build wheels
-        uses: pypa/[email protected].0
+        uses: pypa/[email protected].2
 
       - name: Upload wheels
         uses: actions/upload-artifact@v3
@@ -38,7 +38,7 @@ jobs:
           if-no-files-found: error
 
   build_sdist:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
 
     steps:
       - uses: actions/checkout@v4
@@ -48,7 +48,7 @@ jobs:
           fetch-depth: 0
 
       - name: Install Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: '3.9'
 

.github/workflows/docs.yml

@@ -20,9 +20,10 @@ jobs:
         fetch-depth: 0
 
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: 3.9
+        cache: pip
 
     - name: Build and install at
       run: python -m pip install ".[plot, doc]"

.github/workflows/matlab-tests.yml

@@ -27,9 +27,10 @@ jobs:
     - uses: actions/checkout@v4
 
     - name: Set up python 3.9
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.9'
+        cache: pip
 
     - name: Set up MATLAB
       uses: matlab-actions/setup-matlab@v1

.github/workflows/python-tests.yml

@@ -16,7 +16,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11', '3.12']
         os: [macos-latest, ubuntu-latest, windows-latest]
         exclude:
           - os: windows-latest
@@ -27,9 +27,10 @@ jobs:
     - uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
+        cache: pip
 
     - name: Build and install at with tests
       run: python -m pip install -e ".[dev]"
@@ -39,8 +40,8 @@ jobs:
       run: |
         # stop the build if there are Python syntax errors or undefined names
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+        # exit-zero treats all errors as warnings. Options compatible with the 'black' code formatter
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=88 --extend-ignore=E203,E704 --extend-select=W504 --per-file-ignores='*/__init__.py:F401,F403' --statistics
 
     - name: Test with pytest and coverage
       working-directory: pyat

LICENSE.txt

@@ -0,0 +1 @@
+License pending

_custom_build/backend.py

@@ -1,8 +1,9 @@
-from setuptools import build_meta as _orig
+"""Implements PEP 517 and PEP 660 hooks for custom build"""
+
 import os
 
-# Mandatory hooks
-build_sdist = _orig.build_sdist
+from setuptools import build_meta as _orig
+from setuptools.build_meta import *  # noqa: F401, F403
 
 
 def _get_option(config, key, default_value):
@@ -12,30 +13,43 @@ def _get_option(config, key, default_value):
     return eval(val)
 
 
-def build_wheel(wheel_dir, config_settings=None, metadata_dir=None):
-    print("** Entering build_wheel. "
-          "Config settings:", config_settings)
-    os.environ["MPI"] = str(_get_option(config_settings, 'MPI', '0'))
-    os.environ["OPENMP"] = str(_get_option(config_settings, 'OPENMP', '0'))
-    omp_threshold = _get_option(config_settings,
-                                'OMP_PARTICLE_THRESHOLD', 'None')
-    if omp_threshold is not None:
-        os.environ["OMP_PARTICLE_THRESHOLD"] = str(omp_threshold)
-    print("** MPI:", os.environ.get('MPI', 'None'))
-    print("** OPENMP:", os.environ.get('OPENMP', 'None'))
-    ret = _orig.build_wheel(wheel_dir, config_settings, metadata_dir)
-    print("** Leaving build_wheel")
-    return ret
-
-
-# Optional hook
-def get_requires_for_build_wheel(config_settings=None):
-    print("** Entering get_requires_for_build_wheel. "
-          "Config settings:", config_settings)
-    mpi = _get_option(config_settings, 'MPI', '0')
-    print("** MPI:", mpi)
-    addlist = ["mpi4py"] if mpi else []
-    print("** Additional modules:", addlist)
-    ret = _orig.get_requires_for_build_wheel(config_settings) + addlist
-    print("** Leaving get_requires_for_build_wheel")
-    return ret
+def _set_environ(func):
+    """Set environment for building according to config"""
+
+    def build(wheel_dir, config_settings=None, metadata_dir=None):
+        print("** Entering set_environ. " "Config settings:", config_settings)
+        os.environ["MPI"] = str(_get_option(config_settings, "MPI", "0"))
+        os.environ["OPENMP"] = str(_get_option(config_settings, "OPENMP", "0"))
+        omp_threshold = _get_option(config_settings, "OMP_PARTICLE_THRESHOLD", "None")
+        if omp_threshold is not None:
+            os.environ["OMP_PARTICLE_THRESHOLD"] = str(omp_threshold)
+        print("** MPI:", os.environ.get("MPI", "None"))
+        print("** OPENMP:", os.environ.get("OPENMP", "None"))
+        ret = func(wheel_dir, config_settings, metadata_dir)
+        print("** Leaving set_environ")
+        return ret
+
+    return build
+
+
+def _requirements(func):
+    """Add build requirements according to config"""
+
+    def get_requires(config_settings=None):
+        print("** Entering get_requires. Config settings:", config_settings)
+        mpi = _get_option(config_settings, "MPI", "0")
+        print("** MPI:", mpi)
+        addlist = ["mpi4py"] if mpi else []
+        print("** Additional modules:", addlist)
+        ret = func(config_settings) + addlist
+        print("** Leaving get_requires")
+        return ret
+
+    return get_requires
+
+
+build_wheel = _set_environ(_orig.build_wheel)
+build_editable = _set_environ(_orig.build_editable)
+
+get_requires_for_build_wheel = _requirements(_orig.get_requires_for_build_wheel)
+get_requires_for_build_editable = _requirements(_orig.get_requires_for_build_editable)

atintegrators/BeamLoadingCavityPass.c

@@ -14,6 +14,7 @@ struct elem
   int nturnsw;
   int blmode;
   int cavitymode;
+  int buffersize;
   double normfact;
   double phasegain;
   double voltgain;
@@ -34,7 +35,16 @@ struct elem
   double *vbeam;
   double *vcav;
   double *vgen;
+  double *vgen_buffer;
+  double *vbeam_buffer;
+  double *vbunch_buffer;
 }; 
+
+
+void write_buffer(double *data, double *buffer, int datasize, int buffersize){
+    memmove(buffer, buffer + datasize, datasize*buffersize*sizeof(double));
+    memcpy(buffer + datasize*(buffersize-1), data, datasize*sizeof(double));
+}
 
 
 void BeamLoadingCavityPass(double *r_in,int num_particles,int nbunch,
@@ -48,6 +58,7 @@ void BeamLoadingCavityPass(double *r_in,int num_particles,int nbunch,
     long nslice = Elem->nslice;
     long nturnsw = Elem->nturnsw;
     long blmode = Elem->blmode;
+    long buffersize = Elem->buffersize;
     double normfact = Elem->normfact;  
     double le = Elem->Length;
     double energy = Elem->Energy;
@@ -58,6 +69,9 @@ void BeamLoadingCavityPass(double *r_in,int num_particles,int nbunch,
     double rshunt = Elem->Rshunt;
     double beta = Elem->Beta;
     double *turnhistory = Elem->turnhistory;
+    double *vgen_buffer = Elem->vgen_buffer;
+    double *vbeam_buffer = Elem->vbeam_buffer;
+    double *vbunch_buffer = Elem->vbunch_buffer;
     double *z_cuts = Elem->z_cuts;
     double *vbunch = Elem->vbunch;
     double phasegain = Elem->phasegain;
@@ -89,7 +103,6 @@ void BeamLoadingCavityPass(double *r_in,int num_particles,int nbunch,
     /*Track RF cavity is always done. */
     trackRFCavity(r_in,le,vgen/energy,rffreq,harmn,tlag,-psi,nturn,circumference/C0,num_particles);
 
-    
     /*Only allocate memory if current is > 0*/
     if(tot_current>0){
         void *buffer = atMalloc(sz);
@@ -126,6 +139,11 @@ void BeamLoadingCavityPass(double *r_in,int num_particles,int nbunch,
         if(cavitymode==1){
             update_vgen(vbeamk,vcavk,vgenk,phasegain,voltgain); 
         }
+        if(buffersize>0){
+            write_buffer(vbeamk, vbeam_buffer, 2, buffersize);
+            write_buffer(vgenk, vgen_buffer, 2, buffersize);
+            write_buffer(vbunch, vbunch_buffer, 2*nbunch, buffersize);
+        }
         atFree(buffer);
     }
 }
@@ -138,10 +156,13 @@ ExportMode struct elem *trackFunction(const atElem *ElemData,struct elem *Elem,
     double rl = Param->RingLength;
     int nturn=Param->nturn;
     if (!Elem) {
-        long nslice,nturns,blmode,cavitymode;
+        long nslice,nturns,blmode,cavitymode, buffersize;
         double wakefact;
         double normfact, phasegain, voltgain;
         double *turnhistory;
+        double *vgen_buffer;
+        double *vbeam_buffer;
+        double *vbunch_buffer;
         double *z_cuts;
         double Energy, Frequency, TimeLag, Length;
         double qfactor,rshunt,beta;
@@ -160,6 +181,7 @@ ExportMode struct elem *trackFunction(const atElem *ElemData,struct elem *Elem,
         nslice=atGetLong(ElemData,"_nslice"); check_error();
         nturns=atGetLong(ElemData,"_nturns"); check_error();
         blmode=atGetLong(ElemData,"_blmode"); check_error();
+        buffersize=atGetLong(ElemData,"_buffersize"); check_error();
         cavitymode=atGetLong(ElemData,"_cavitymode"); check_error();
         wakefact=atGetDouble(ElemData,"_wakefact"); check_error();
         qfactor=atGetDouble(ElemData,"Qfactor"); check_error();
@@ -174,6 +196,9 @@ ExportMode struct elem *trackFunction(const atElem *ElemData,struct elem *Elem,
         vcav=atGetDoubleArray(ElemData,"_vcav"); check_error();
         vgen=atGetDoubleArray(ElemData,"_vgen"); check_error();
         vbeam_phasor=atGetDoubleArray(ElemData,"_vbeam_phasor"); check_error(); 
+        vgen_buffer=atGetDoubleArray(ElemData,"_vgen_buffer"); check_error();
+        vbeam_buffer=atGetDoubleArray(ElemData,"_vbeam_buffer"); check_error();
+        vbunch_buffer=atGetDoubleArray(ElemData,"_vbunch_buffer"); check_error();
         /*optional attributes*/
 
         z_cuts=atGetOptionalDoubleArray(ElemData,"ZCuts"); check_error();
@@ -207,6 +232,10 @@ ExportMode struct elem *trackFunction(const atElem *ElemData,struct elem *Elem,
         Elem->voltgain = voltgain;
         Elem->vbeam_phasor = vbeam_phasor;
         Elem->cavitymode = cavitymode;
+        Elem->buffersize = buffersize;
+        Elem->vgen_buffer = vgen_buffer;
+        Elem->vbeam_buffer = vbeam_buffer;
+        Elem->vbunch_buffer = vbunch_buffer;
     }
     if(num_particles<Param->nbunch){
         atError("Number of particles has to be greater or equal to the number of bunches.");
@@ -245,7 +274,7 @@ void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
       int num_particles = mxGetN(prhs[1]);
       struct elem El, *Elem=&El;
 
-      long nslice,nturns,blmode,cavitymode;
+      long nslice,nturns,blmode,cavitymode, buffersize;
       double wakefact;
       double normfact, phasegain, voltgain;
       double *turnhistory;
@@ -257,6 +286,9 @@ void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
       double *vbeam;
       double *vgen;
       double *vcav;
+      double *vgen_buffer;
+      double *vbeam_buffer;
+      double *vbunch_buffer;
       /*attributes for RF cavity*/
       Length=atGetDouble(ElemData,"Length"); check_error();
       Energy=atGetDouble(ElemData,"Energy"); check_error();
@@ -266,6 +298,7 @@ void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
       nslice=atGetLong(ElemData,"_nslice"); check_error();
       nturns=atGetLong(ElemData,"_nturns"); check_error();
       blmode=atGetLong(ElemData,"_blmode"); check_error();
+      buffersize=atGetLong(ElemData,"_buffersize"); check_error();
       cavitymode=atGetLong(ElemData,"_cavitymode"); check_error();
       wakefact=atGetDouble(ElemData,"_wakefact"); check_error();
       qfactor=atGetDouble(ElemData,"Qfactor"); check_error();
@@ -280,6 +313,9 @@ void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
       vcav=atGetDoubleArray(ElemData,"_vcav"); check_error();
       vgen=atGetDoubleArray(ElemData,"_vgen"); check_error();
       vbeam_phasor=atGetDoubleArray(ElemData,"_vbeam_phasor"); check_error(); 
+      vgen_buffer=atGetDoubleArray(ElemData,"_vgen_buffer"); check_error();
+      vbeam_buffer=atGetDoubleArray(ElemData,"_vbeam_buffer"); check_error();
+      vbunch_buffer=atGetDoubleArray(ElemData,"_vbunch_buffer"); check_error();
       /*optional attributes*/
       z_cuts=atGetOptionalDoubleArray(ElemData,"ZCuts"); check_error();
 
@@ -306,6 +342,10 @@ void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
       Elem->phasegain = phasegain;
       Elem->voltgain = voltgain;
       Elem->vbeam_phasor = vbeam_phasor;
+      Elem->buffersize = buffersize;
+      Elem->vgen_buffer = vgen_buffer;
+      Elem->vbeam_buffer = vbeam_buffer;
+      Elem->vbunch_buffer = vbunch_buffer;
 
       if (mxGetM(prhs[1]) != 6) mexErrMsgIdAndTxt("AT:WrongArg","Second argument must be a 6 x N matrix");
       /* ALLOCATE memory for the output array of the same size as the input  */
@@ -318,7 +358,7 @@ void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
   }
   else if (nrhs == 0)
   {   /* return list of required fields */
-      plhs[0] = mxCreateCellMatrix(19,1);
+      plhs[0] = mxCreateCellMatrix(24,1);
       mxSetCell(plhs[0],0,mxCreateString("Length"));
       mxSetCell(plhs[0],1,mxCreateString("Energy"));
       mxSetCell(plhs[0],2,mxCreateString("Frequency"));
@@ -339,6 +379,10 @@ void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
       mxSetCell(plhs[0],17,mxCreateString("_vcav"));
       mxSetCell(plhs[0],18,mxCreateString("_vgen"));
       mxSetCell(plhs[0],19,mxCreateString("_vbeam_phasor"));
+      mxSetCell(plhs[0],20,mxCreateString("_vgen_buffer"));
+      mxSetCell(plhs[0],21,mxCreateString("_vbeam_buffer"));
+      mxSetCell(plhs[0],22,mxCreateString("_vbunch_buffer"));
+      mxSetCell(plhs[0],23,mxCreateString("_buffersize"));
       if(nlhs>1) /* optional fields */
       {
           plhs[1] = mxCreateCellMatrix(2,1);