Merge pull request #32 from rikigigi/devel

Devel
rikigigi · Apr 26, 2023 · 7b68dad · 7b68dad
2 parents ce11cc6 + 6177cb5
commit 7b68dad
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diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
@@ -21,7 +21,7 @@ jobs:
     strategy:
         matrix:
             os: [ubuntu-latest, macos-latest ]
-            python-version: [ "3.7" ] 
+            python-version: [ "3.7", "3.11" ] 
     steps:
     - uses: actions/checkout@v3
       with:
@@ -72,7 +72,7 @@ jobs:
     strategy:
         matrix:
             os: [windows-latest ]
-            python-version: [ "3.7" ] 
+            python-version: [ "3.7", "3.11" ] 
     steps:
     - uses: actions/checkout@v2
       with:

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -265,7 +265,7 @@ if(PYTHON_INTERFACE)
 if (${PYTHONLIBS_FOUND})
 #python interface
 set (PYTHON_SUPPORT ${PYTHON_LIBRARIES})
-#target_link_libraries(${PROJECT_NAME} PRIVATE pybind11::module)
+target_link_libraries(${PROJECT_NAME}_lib PUBLIC pybind11::embed)
 INCLUDE_DIRECTORIES(${PYTHON_INCLUDE_DIRS})
 include_directories(pybind11/include)
 include_directories(${CMAKE_CURRENT_SOURCE_DIR})

diff --git a/README.md b/README.md
@@ -159,6 +159,7 @@ Calculations:
 If you clone the repository you have to initialize the submodules with
 
 	git submodule init
+        git submodule update
 
 this will initialize the pybind11 repository for the (optional) python interface
 Dependencies:

diff --git a/README.pdf b/README.pdf
diff --git a/README_.md b/README_.md
@@ -159,6 +159,7 @@ Calculations:
 If you clone the repository you have to initialize the submodules with
 
 	git submodule init
+        git submodule update
 
 this will initialize the pybind11 repository for the (optional) python interface
 Dependencies:

diff --git a/config.h.in b/config.h.in
@@ -47,7 +47,7 @@
 #endif
 
 const static char * _info_msg=
-"cite as:\nRiccardo Bertossa, analisi\nhttps://github.com/rikigigi/analisi\n(c) 2017-2022\n=========\n"
+"cite as:\nRiccardo Bertossa, analisi\nhttps://github.com/rikigigi/analisi\n(c) 2017-2023\n=========\n"
  "COMPILED AT " __DATE__ " " __TIME__ " by " CMAKE_CXX_COMPILER " whith flags (Release)"
              CMAKE_CXX_FLAGS  " " CMAKE_CXX_FLAGS_RELEASE " (Debug) " CMAKE_CXX_FLAGS  " " CMAKE_CXX_FLAGS_DEBUG " (build type was " CMAKE_BUILD_TYPE ")"
              " on a " CMAKE_SYSTEM " whith processor " CMAKE_SYSTEM_PROCESSOR
@@ -60,7 +60,7 @@ const static char * _info_msg=
 #ifdef XDR_FILE
 "\nWith gromacs XDR file conversion support"
 #endif
-"\nv0.5.0"
+"\nv0.5.1"
 ;
 
 

diff --git a/install/install_test.sh b/install/install_test.sh
@@ -1,3 +1,3 @@
 #!/bin/bash
 set -e
-pip install pytest pytest-regressions==2.2.0 pandas matplotlib numpy scipy testbook k3d
+pip install pytest pytest-regressions pandas matplotlib numpy scipy testbook k3d
diff --git a/lib/include/atomicdensity.h b/lib/include/atomicdensity.h
@@ -32,7 +32,7 @@ class AtomicDensity : public CalculateMultiThread<AtomicDensity<T,Hist>>, public
     T * t;
     size_t ntypes;
     size_t idx(const size_t x, const size_t y, const size_t z, const size_t itype) const {
-        return x + nbin[2]*(y + nbin[1]*(z + itype*nbin[0]));
+        return x + nbin[0]*(y + nbin[1]*(z + itype*nbin[2]));
     }
     size_t idx_(const double * pos, const double * l, bool & ok,int itype) const {
         size_t idxs[3];
@@ -49,7 +49,7 @@ class AtomicDensity : public CalculateMultiThread<AtomicDensity<T,Hist>>, public
             }
             idxs[icoord] = std::floor(l_*nbin[icoord]);
         }
-        return idx(idxs[2],idxs[1],idxs[0],itype);
+        return idx(idxs[0],idxs[1],idxs[2],itype);
     }
 
     using CalculateMultiThread<This>::ntimesteps;

diff --git a/lib/include/buffer_utils.h b/lib/include/buffer_utils.h
@@ -1,3 +1,7 @@
+#ifndef BUFFER_UTILS_H
+#define BUFFER_UTILS_H
+
+#include "compiler_types.h"
 
 template <typename T>
 bool has_no_stride(const pybind11::buffer_info & buf) {
@@ -9,3 +13,5 @@ bool has_no_stride(const pybind11::buffer_info & buf) {
     }
     return true;
 }
+
+#endif
diff --git a/lib/include/compiler_types.h b/lib/include/compiler_types.h
@@ -1,4 +1,9 @@
+#ifndef COMPILER_TYPES_H
+#define COMPILER_TYPES_H
+
 #if defined(_MSC_VER)
 #include <BaseTsd.h>
 typedef SSIZE_T ssize_t;
-#endif
+#endif
+
+#endif
diff --git a/lib/src/atomicdensity.cpp b/lib/src/atomicdensity.cpp
@@ -60,11 +60,11 @@ void  AtomicDensity<T,Hist>::reset(const unsigned int numeroTimestepsPerBlocco)
 }
 template <class T, class Hist>
 std::vector<ssize_t>  AtomicDensity<T,Hist>::get_shape() const{
-    return {static_cast<long>(ntypes),static_cast<long>(nbin[0]),static_cast<long>(nbin[1]),static_cast<long>(nbin[2])};
+    return {static_cast<long>(ntypes),static_cast<long>(nbin[2]),static_cast<long>(nbin[1]),static_cast<long>(nbin[0])};
 }
 template <class T, class Hist>
 std::vector<ssize_t>  AtomicDensity<T,Hist>::get_stride() const {
-    return {static_cast<long>(sizeof (Hist))*static_cast<long>(nbin[0]*nbin[1]*nbin[2]),static_cast<long>(nbin[1]*nbin[2]*sizeof (Hist)),static_cast<long>(nbin[2]*sizeof (Hist)),static_cast<long>(sizeof (Hist))};
+    return {static_cast<long>(sizeof (Hist))*static_cast<long>(nbin[0]*nbin[1]*nbin[2]),static_cast<long>(nbin[1]*nbin[0]*sizeof (Hist)),static_cast<long>(nbin[0]*sizeof (Hist)),static_cast<long>(sizeof (Hist))};
 }
 
 #ifdef BUILD_MMAP

diff --git a/lib/src/gofrt.cpp b/lib/src/gofrt.cpp
@@ -17,6 +17,7 @@
 #include <fstream>
 #include <sstream>
 #include "config.h"
+#include "mp.h"
 
 template <class TFLOAT,class T> Gofrt<TFLOAT,T>::Gofrt(T *t, TFLOAT rmin, TFLOAT rmax, unsigned int nbin, unsigned int tmax, unsigned int nthreads, unsigned int skip,unsigned int every, bool debug) :
     CalculateMultiThread_T {nthreads, skip, t->get_natoms(), every},

diff --git a/lib/src/sphericalbase.cpp b/lib/src/sphericalbase.cpp
@@ -100,13 +100,25 @@ void SphericalBase<lmax,TFLOAT,T>::calc(int timestep,
 #include "config.h"
 #ifdef BUILD_MMAP
 #include "trajectory.h"
+template class SphericalBase<2,double,Trajectory>;
+template class SphericalBase<3,double,Trajectory>;
+template class SphericalBase<4,double,Trajectory>;
+template class SphericalBase<5,double,Trajectory>;
 template class SphericalBase<6,double,Trajectory>;
+template class SphericalBase<7,double,Trajectory>;
 template class SphericalBase<8,double,Trajectory>;
+template class SphericalBase<9,double,Trajectory>;
 template class SphericalBase<10,double,Trajectory>;
 #endif
 #ifdef PYTHON_SUPPORT
 #include "trajectory_numpy.h"
+template class SphericalBase<2,double,Trajectory_numpy>;
+template class SphericalBase<3,double,Trajectory_numpy>;
+template class SphericalBase<4,double,Trajectory_numpy>;
+template class SphericalBase<5,double,Trajectory_numpy>;
 template class SphericalBase<6,double,Trajectory_numpy>;
+template class SphericalBase<7,double,Trajectory_numpy>;
 template class SphericalBase<8,double,Trajectory_numpy>;
+template class SphericalBase<9,double,Trajectory_numpy>;
 template class SphericalBase<10,double,Trajectory_numpy>;
 #endif
diff --git a/lib/src/steinhardt.cpp b/lib/src/steinhardt.cpp
@@ -253,13 +253,25 @@ void Steinhardt<l,TFLOAT,T>::join_data() {
 
 #ifdef BUILD_MMAP
 #include "trajectory.h"
+template class Steinhardt<2,double,Trajectory>;
+template class Steinhardt<3,double,Trajectory>;
+template class Steinhardt<4,double,Trajectory>;
+template class Steinhardt<5,double,Trajectory>;
 template class Steinhardt<6,double,Trajectory>;
+template class Steinhardt<7,double,Trajectory>;
 template class Steinhardt<8,double,Trajectory>;
+template class Steinhardt<9,double,Trajectory>;
 template class Steinhardt<10,double,Trajectory>;
 #endif
 #ifdef PYTHON_SUPPORT
 #include "trajectory_numpy.h"
+template class Steinhardt<2,double,Trajectory_numpy>;
+template class Steinhardt<3,double,Trajectory_numpy>;
+template class Steinhardt<4,double,Trajectory_numpy>;
+template class Steinhardt<5,double,Trajectory_numpy>;
 template class Steinhardt<6,double,Trajectory_numpy>;
+template class Steinhardt<7,double,Trajectory_numpy>;
 template class Steinhardt<8,double,Trajectory_numpy>;
+template class Steinhardt<9,double,Trajectory_numpy>;
 template class Steinhardt<10,double,Trajectory_numpy>;
 #endif
diff --git a/notebooks/example2.ipynb b/notebooks/example2.ipynb
@@ -0,0 +1,135 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%load_ext autoreload\n",
+    "%autoreload 2\n",
+    "from pyanalisi import *\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Load the binary trajectory in one shot\n",
+    "\n",
+    "can be done better if less RAM usage is needed"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "phase_IV=read_lammps_bin('./dump2.8fs.bin',wrap=False)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "phase_IV.get_array('positions').shape"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "plt.plot(phase_IV.get_array('positions')[:,phase_IV.t.get_lammps_type()==1,0][:,:10])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "pl=show_traj(phase_IV,wrap=False)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "scrolled": false
+   },
+   "outputs": [],
+   "source": [
+    "res=multiinspect([phase_IV], plot=True, prefix='phase_IV_nose_',\n",
+    "                 inspect_kw={\n",
+    "                     'nthreads':12,\n",
+    "                     'do_sh':False,\n",
+    "                     'plot_st_kw': {\n",
+    "                         'transpose':True,\n",
+    "                         'xmax':.40,\n",
+    "                         'ymax':.70,\n",
+    "                         'single':(1,1),\n",
+    "                         'plt_points':[(0.15818,0.491385,0.05,{'alpha':0.5,'fill':True,'ls':':','color':'blue'}),#fcc\n",
+    "                                      (0.084052,0.421813,0.05,{'alpha':0.5,'fill':True,'ls':':','color':'green'})#hcp\n",
+    "                                    ]\n",
+    "                     },\n",
+    "                     'compute_steinhardt_kw':{'skip':40},\n",
+    "                     \n",
+    "                 })"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%matplotlib notebook"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "scrolled": false
+   },
+   "outputs": [],
+   "source": [
+    "steinhardt_movie(phase_IV,skip=20,n_segments=150,\n",
+    "                 plt_steinhardt_kw={\n",
+    "                         'transpose':True,\n",
+    "                         'xmax':.40,\n",
+    "                         'ymax':.70,\n",
+    "                         'single':(1,1)},\n",
+    "                 compute_steinhardt_kw={'nthreads':12},\n",
+    "                 neigh=[(55,3.5**2,0.0),(65,3.5**2,0.0)]\n",
+    "                )"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.7.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}