Merge branch 'develop'

.gitignore

@@ -1,3 +1,5 @@
+*.log
+*.aux
 geom_impact_poly_cython.c
 boris_cython.c
 #*.beam
@@ -20,4 +22,4 @@ scripts/
 *.h5part
 .ipynb_checkpoints
 Pyecltest.mat
-
+*.png

doc/example/000_plot_main_output.py

@@ -0,0 +1,257 @@
+# generate example figures with main PyECLOUD outputs
+# Thanks for E. Belli, L. Mether and A. Romano for preparing this script
+
+import sys, os
+BIN = os.path.expanduser("../../../")
+sys.path.append(BIN)
+
+import pylab as pl
+import numpy as np
+
+import PyECLOUD.myloadmat_to_obj as mlo
+import PyECLOUD.mystyle as ms
+
+pl.close('all')
+ms.mystyle_arial(fontsz=16)
+dpiset = 200
+
+ob=mlo.myloadmat_to_obj('../../testing/tests_buildup/LHC_ArcDipReal_450GeV_sey1.60_2.5e11ppb_bl_1.00ns/Pyecltest_ref.mat')
+
+ifig = 0
+
+#################################
+# Variables saved per time step #
+#################################
+
+#8.
+ifig+=1; pl.figure(ifig)
+pl.plot(ob.t, ob.lam_t_array, linewidth=2)
+pl.xlabel('Time [s]')
+pl.ylabel('Beam profile [p/m]') 
+ms.scix(); pl.grid('on')
+pl.suptitle('Var. name: lam_t_array\nBeam density at each time step')
+pl.subplots_adjust(top=.82, bottom=.14)
+pl.savefig('fig%02d.png'%ifig, dpi=dpiset)
+
+#6.
+ifig+=1; pl.figure(ifig)
+pl.plot(ob.t, ob.Nel_timep, linewidth=2)
+pl.xlabel('Time [s]')
+pl.ylabel('Number of $e^-$ per unit length [$m^{-1}$]') 
+ms.scix(); pl.grid('on')
+pl.suptitle('Var. name: Nel_timep\nNumber of electrons in the chamber at each time step')
+pl.subplots_adjust(top=.82, bottom=.14)
+pl.savefig('fig%02d.png'%ifig, dpi=dpiset)
+
+#5.
+ifig+=1; pl.figure(ifig)
+pl.plot(ob.t, ob.Nel_imp_time, linewidth=2)
+pl.xlabel('Time [s]')
+pl.ylabel('Number of impacting $e^-$ per unit length [$m^{-1}$]') 
+ms.scix(); pl.grid('on')
+pl.suptitle('Var. name: Nel_imp_time\nNumber of electrons that impact the walls in each time-step')
+pl.subplots_adjust(top=.82, bottom=.14)
+pl.savefig('fig%02d.png'%ifig, dpi=dpiset)
+
+#4.
+ifig+=1; pl.figure(ifig)
+pl.plot(ob.t, ob.Nel_emit_time, linewidth=2)
+pl.xlabel('Time [s]')
+pl.ylabel('Number of emitted $e^-$ per unit length [$m^{-1}$]') 
+ms.scix(); pl.grid('on')
+pl.suptitle('Var. name: Nel_emit_time\nNumber of electrons emitted by walls in each time-step')
+pl.subplots_adjust(top=.82, bottom=.14)
+pl.savefig('fig%02d.png'%ifig, dpi=dpiset)
+
+#2. 
+ifig+=1; pl.figure(ifig)
+pl.plot(ob.t, ob.En_imp_eV_time, linewidth=2)
+pl.xlabel('Time [s]')
+pl.ylabel('Deposited electron energy [eV]') 
+ms.scix(); pl.grid('on')
+pl.suptitle('Var. name: En_imp_eV_time\nElectron energy deposited on the walls in each time-step')
+pl.subplots_adjust(top=.82, bottom=.14)
+pl.savefig('fig%02d.png'%ifig, dpi=dpiset)
+
+#1. 
+ifig+=1; pl.figure(ifig)
+pl.plot(ob.t, ob.En_emit_eV_time, linewidth=2)
+pl.xlabel('Time [s]')
+pl.ylabel('Emitted electron energy [eV]') 
+ms.scix(); pl.grid('on')
+pl.suptitle('Var. name: En_emit_eV_time\nElectron energy emitted by the walls in each time-step')
+pl.subplots_adjust(top=.82, bottom=.14)
+pl.savefig('fig%02d.png'%ifig, dpi=dpiset)
+
+#3.
+ifig+=1; pl.figure(ifig)
+pl.plot(ob.t, ob.En_kin_eV_time, linewidth=2)
+pl.xlabel('Time [s]')
+pl.ylabel('$e^-$ kinetic energy [eV]') 
+ms.scix(); pl.grid('on')
+pl.suptitle('Var. name: En_kin_eV_time\nTotal kinetic energy of the electrons at each time-step')
+pl.subplots_adjust(top=.82, bottom=.14)
+pl.savefig('fig%02d.png'%ifig, dpi=dpiset)
+
+#7.
+ifig+=1; pl.figure(ifig)
+pl.plot(ob.t, ob.cen_density, linewidth=2)
+pl.xlabel('Time [s]')
+pl.ylabel('$e^-$ density [$m^{-3}$]')
+ms.scix(); pl.grid('on')
+pl.suptitle('Var. name: cen_density\nelectron density at the beam position')
+pl.subplots_adjust(top=.82, bottom=.14)
+pl.savefig('fig%02d.png'%ifig, dpi=dpiset)
+
+
+###############################
+# Variables saved per passage #
+###############################
+
+#15.
+ifig+=1; pl.figure(ifig)
+pl.plot(ob.N_mp_pass, linewidth=2) 
+pl.xlabel('Passage')
+pl.ylabel('Number of MP per unit length [$m^{-1}$]') 
+ms.scix(); ms.sciy(); pl.grid('on')
+pl.suptitle('Var. name: N_mp_pass\nNumber of MP at each passage')
+pl.subplots_adjust(top=.82, bottom=.14)
+pl.savefig('fig%02d.png'%ifig, dpi=dpiset)
+
+#16.
+ifig+=1; pl.figure(ifig)
+pl.plot(ob.N_mp_impact_pass, linewidth=2) 
+pl.xlabel('Passage')
+pl.ylabel('Number of impacting MP per passage') 
+pl.grid('on');ms.sciy()
+pl.suptitle('Var. name: N_mp_impact_pass\nNumber of macroparticles that impact for each passage')
+pl.subplots_adjust(top=.82, bottom=.14)
+pl.savefig('fig%02d.png'%ifig, dpi=dpiset)
+
+#17.
+ifig+=1; pl.figure(ifig)
+pl.plot(ob.N_mp_corrected_pass, linewidth=2)
+pl.xlabel('Passage')
+pl.ylabel('Number of corrected MP per passage') 
+pl.grid('on');ms.sciy()
+pl.suptitle('Var. name: N_mp_corrected_pass\nNumber of macroparticles for which fallback algorithm is used.')
+pl.subplots_adjust(top=.82, bottom=.14)
+pl.savefig('fig%02d.png'%ifig, dpi=dpiset)
+
+#18.
+ifig+=1; pl.figure(ifig)
+pl.plot(ob.N_mp_ref_pass, linewidth=2)
+pl.xlabel('Passage')
+pl.ylabel('Reference MP size') 
+pl.grid('on');ms.sciy()
+pl.suptitle('Var. name: N_mp_ref_pass\nReference macroparticle size at each passage')
+pl.subplots_adjust(top=.82, bottom=.14)
+pl.savefig('fig%02d.png'%ifig, dpi=dpiset)
+
+
+###############################
+# Variables saved in matrices #
+#   (Projections are shown)   #
+###############################
+
+#The output file also contains variables represented by matrices with dimension (t_hist, xg_hist) where t_hist[i] represent the time
+#right before the i-th passage in the machine and xg_hist[i] represents the position of the i-th slice inside the chamber
+#--> dim(t_hist)=#passages, dim(xg_hist)=#slices 
+
+
+#P |----------------------|
+#A |----------------------|
+#S |----------------------|
+#S |----------------------|
+#A |----------------------|
+#G |----------------------|
+#E |----------------------|
+            #SLICE
+
+#9.
+ifig+=1; pl.figure(ifig)
+pl.plot(np.sum(ob.nel_hist, axis=1), linewidth=2) #axis=1: sum w.r.t. columns
+pl.xlabel('Passage')
+pl.ylabel('Number of $e^-$ per unit length [$m^{-1}$]') 
+ms.scix(); pl.grid('on')
+pl.suptitle('Var. name: sum(nel_hist, axis=1)\nNumber of electrons at each passage')
+pl.subplots_adjust(top=.82, bottom=.14)
+pl.savefig('fig%02d.png'%ifig, dpi=dpiset)
+
+#10.
+ifig+=1; pl.figure(ifig)
+pl.plot(ob.xg_hist, np.sum(ob.nel_hist, axis=0), linewidth=2) #axis=0: sum w.r.t. rows
+pl.xlabel('Chamber bin position [m]')
+pl.ylabel('Number of $e^-$ per bin') 
+ms.scix(); pl.grid('on')
+pl.suptitle('Var. name: sum(nel_hist, axis=0)\nnumber of electrons in each slice')
+pl.subplots_adjust(top=.82, bottom=.14)
+pl.savefig('fig%02d.png'%ifig, dpi=dpiset)
+
+#11.
+ifig+=1; pl.figure(ifig)
+pl.plot(np.sum(ob.nel_impact_hist_scrub, axis=1), linewidth=2) 
+pl.xlabel('Passage')
+pl.ylabel('Number of impacting scrubbing $e^-$')
+ms.scix(); pl.grid('on')
+pl.suptitle('Var. name: np.sum(ob.nel_impact_hist_scrub, axis=1)\nNumber of impacting scrubbing electrons [E>E_scrub]')
+pl.subplots_adjust(top=.82, bottom=.14)
+pl.savefig('fig%02d.png'%ifig, dpi=dpiset)
+
+#12.
+ifig+=1; pl.figure(ifig)
+pl.plot(ob.xg_hist, np.sum(ob.nel_impact_hist_scrub, axis=0), linewidth=2) 
+pl.xlabel('Chamber bin position [m]')
+pl.ylabel('Impacting scrubbing $e^-$ per bin')
+ms.scix(); pl.grid('on')
+pl.suptitle('Var. name: sum(nel_impact_hist_scrub, axis=0)\nImpacting scrubbing electrons in each slice')
+pl.subplots_adjust(top=.82, bottom=.14)
+pl.savefig('fig%02d.png'%ifig, dpi=dpiset)
+
+#13.
+ifig+=1; pl.figure(ifig)
+pl.plot(np.sum(ob.nel_impact_hist_tot, axis=1), linewidth=2) 
+pl.xlabel('Passage')
+pl.ylabel('Number of impacting $e^-$ per unit length [$m^{-1}$]') 
+ms.scix(); pl.grid('on')
+pl.suptitle('Var. name: sum(nel_impact_hist_tot, axis=1)\nNumber of impacting electrons at each passage')
+pl.subplots_adjust(top=.82, bottom=.14)
+pl.savefig('fig%02d.png'%ifig, dpi=dpiset)
+
+#14.
+ifig+=1; pl.figure(ifig)
+pl.plot(ob.xg_hist, np.sum(ob.nel_impact_hist_tot, axis=0), linewidth=2)
+pl.xlabel('Chamber bin position [m]')
+pl.ylabel('Impacting $e^-$ per bin')
+ms.scix(); pl.grid('on')
+pl.suptitle('Var. name: sum(nel_impact_hist_tot, axis=0)\nNumber of impacting electrons in each slice')
+pl.subplots_adjust(top=.82, bottom=.14)
+pl.savefig('fig%02d.png'%ifig, dpi=dpiset)
+
+#19.
+ifig+=1; pl.figure(ifig)
+pl.plot(np.sum(ob.energ_eV_impact_hist, axis=1), linewidth=2)
+pl.xlabel('Passage')
+pl.ylabel('Energy of impacting electrons [eV]') 
+pl.grid('on');ms.sciy()
+pl.suptitle('Var. name: sum(energ_eV_impact_hist, axis=1)\nEnergy of impacting electrons at each passage')
+pl.subplots_adjust(top=.82, bottom=.14)
+pl.savefig('fig%02d.png'%ifig, dpi=dpiset)
+
+#20.
+ifig+=1; pl.figure(ifig)
+pl.plot(ob.xg_hist, np.sum(ob.energ_eV_impact_hist, axis=0), linewidth=2)
+pl.xlabel('Position in the chamber [m]')
+pl.ylabel('Energy of impacting electrons[eV]') 
+pl.grid('on');ms.sciy(); ms.scix()
+pl.suptitle('Var. name: sum(energ_eV_impact_hist, axis=0)\nTotal energy of impacting electrons per passage [eV]')
+pl.subplots_adjust(top=.82, bottom=.14)
+pl.savefig('fig%02d.png'%ifig, dpi=dpiset)
+
+
+pl.show()
+
+
+
+
+

doc/reference/src/compile_it

@@ -0,0 +1,8 @@
+#!/bin/bash
+
+pdflatex reference.tex
+pdflatex reference.tex
+pdflatex reference.tex
+pdflatex reference.tex
+
+mv reference.pdf ../