moment of interia files

py/mains/uns_plot_inert.py

+#!/usr/bin/env python
+from __future__ import print_function
+
+import numpy as np
+import os,time
+import sys
+import argparse,textwrap
+
+#sys.path=['/home/jcl/works/GIT/uns_projects/py/modules/','/home/jcl/works/GIT/uns_projects/py/modules/simulations']+sys.path
+
+import simulations.cplotinert as pmoi
+
+#from IPython import embed
+
+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+# commandLine, parse the command line 
+def commandLine():
+
+    # help
+    parser = argparse.ArgumentParser(description="Display Moment of Inertia results",
+                                     formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+
+    parser.add_argument('simname', help="uns input simulation name",default=None)
+    parser.add_argument('--component', help="selected component",default="halo")
+    parser.add_argument('--ncut', help="#cuts ",default=20,type=int)
+    parser.add_argument('--outfile', help="output file name",default=None)
+    parser.add_argument('--nodisp', help='dont display on screen',dest="nodisp", action="store_true", default=False)
+    parser.add_argument('--noprogress', help='dont display a progress bar',dest="noprogress", action="store_true", default=False)
+    parser.add_argument('--verbose',help='verbose mode',dest="verbose", action="store_true", default=False)
+
+    # parse
+    args = parser.parse_args()
+    # start main function
+    process(args)
+
+# -----------------------------------------------------
+# process, is the core function
+def process(args):
+
+    try:
+        pinert=pmoi.CPlotInert(args.simname,component=args.component,ncut=args.ncut, progress=not args.noprogress,
+                                 disp=not args.nodisp,outfile=args.outfile,verbose_debug=args.verbose)
+    except Exception as x :
+        print (x.message,file=sys.stderr)
+    except KeyboardInterrupt:
+        sys.exit()
+
+# -----------------------------------------------------
+# main program
+if __name__ == '__main__':
+  commandLine()

py/modules/simulations/cinert.py

+#!/usr/bin/python
+from __future__ import print_function
+from ctree import * 
+from csnapshot import *
+from uns_simu import *
+from ccod import *
+from cfalcon import *
+
+import time
+import os,sys
+import numpy as np
+import math
+import time
+import numpy.linalg as linalg
+#from IPython import embed
+
+#
+# ----
+#
+class CInert:
+    """
+    Compute moment of Inertia
+    """
+    #
+    # ----
+    #
+    # constructor
+    __analysis=None
+    __res_file_name=None
+    __res_fdesc=None
+    __inert_dir="./"
+    __outfile_main=None
+    __snapshot=None
+    __outfile=None
+    __ncut=None
+    __fract_min=None
+    __fract_max=None
+    __com=None
+    __component=None
+    __center_file=None
+
+    def __init__(self,analysis=None,snapshot=None,outfile=None,ncut=10, fract_min=0.1,fract_max=0.9,
+                 com=True,component=None,center_file=None,tree_density=True,tree_threshold=-10., nonemo=False,
+                 verbose=False,verbose_debug=False):
+        """
+        Constructor of CInert class
+
+        - analysis : is a class object instantiate from CUnsAnalysis class
+        """
+
+        self.__vdebug=verbose_debug
+        self.__verbose=verbose
+
+        self.__snapshot=snapshot
+        self.__outfile=outfile
+        self.__ncut=ncut
+        self.__fract_min=fract_min
+        self.__fract_max=fract_max
+        self.__com=com
+        self.__component=component
+        self.__center_file=center_file
+        self.__nonemo=nonemo
+        print("SELF_NONEMO = ",self.__nonemo)
+
+        self.__tree_density   = tree_density
+        self.__tree_threshold = tree_threshold
+        if analysis is None and snapshot is None:
+            #import inspect
+            raise Exception(__file__+": Error, analysis and snapshot are both None..")
+
+        if analysis is not None:
+            self.__analysis=analysis
+            self.__smartAnalysisInit()
+        else: # standalone (full process)
+            # open file
+            self.__res_fdesc = self.__buildRes(outfile,snapshot)
+        
+    # 
+    # smartAnalysisInit
+    #
+    def __smartAnalysisInit(self):
+        """
+        start some initialisations
+        """
+
+        data=self.__analysis
+
+        ### build INERT Dir
+        if hasattr(data,'inert_dir'):
+            self.__inert_dir=data.inert_dir
+            #
+        else: # default simdir simulation
+            self.__inert_dir=data.sim_info['dir']+"/ANALYSIS/inert"
+
+        print("INERT DIR = ", self.__inert_dir, data.sim_info['name'])
+        self.simname=data.sim_info['name']
+        #self.__com_file_base=self.__inert_dir
+
+        # lock process
+        data.lock[data.lock_id].acquire()
+        # outfile
+        self.__outfile_main = self.simname+"_inertN_"+self.__component+".res"
+        self.__outfile_head = self.__inert_dir+"/HEAD_"+self.__outfile_main
+
+        # build directory
+        if (not os.path.isdir(self.__inert_dir) or not os.path.exists(self.__outfile_head)) :
+            try:
+                print("Core ID ",data.core_id," create directory [%s]\n"%(self.__inert_dir))
+                os.makedirs(self.__inert_dir)
+                os.makedirs(self.__inert_dir+"/.parallel")
+
+                # save HEAD
+                try:
+                    print("Saving header [%s]\n"%(self.__outfile_head ),file=sys.stderr)
+                    f=open(self.__outfile_head,"w")
+                    f.write("%s\n%d\n"%(self.simname,self.__ncut))
+                    f.close()
+                except:
+                    print("\n\nUnable to save inert_file[%s] ... aborting...\n"%(self.__outfile_head),file=sys.stderr)
+                    sys.exit()
+
+            except OSError:
+                print("Unable to create directory [%s]\n"%(self.__inert_dir))
+                data.lock[data.lock_id].release()
+                sys.exit()
+
+        # release process
+        data.lock[data.lock_id].release()
+        
+
+    #
+    #
+    #
+    def __buildRes(self,outfile,simname):
+        """
+        build outfile name
+
+        Return :
+        file descriptor
+        """
+        if outfile is None:
+            self.__res_filen_name=simname+"_inertN_"+self.__component+".res"
+        else:
+            self.__res_filen_name=outfile
+
+        try:
+            self.__fdesc=open(self.__res_filen_name,"w")
+        except :#IOError :
+            print("Unable to open file [%s]\n"%(self.__res_filen_name),file=sys.stderr)
+            sys.exit()
+        return self.__fdesc
+
+    #
+    #
+    #
+    def fullProcess(self,snapshot,component):
+        """
+        Run full process on input snapshot
+        """
+        class CData:
+            uns_snap=None
+            single_proc=True
+            first=True
+            lock=[Lock()]
+            lock_id=0
+
+        analysis = CData() # instantiate CData object to mimic online analysis 
+        
+
+        self.__analysis=analysis
+
+        self.__fdesc.write("%s\n%d\n"%(snapshot,self.__ncut)) # save header
+
+        # instantiate CSnapshot
+        uns=CSnapshot(snapshot,component,verbose_debug=self.__vdebug)
+        # fill up analysis object
+        analysis.uns_snap=uns
+
+        # loop on snapshots
+        n = 0
+        while(uns.nextFrame("")):
+            analysis.snap_id = n
+            self.smartAnalysis(analysis)
+            n = n + 1
+
+        # close outfile
+        self.__fdesc.close()
+
+        
+    # 
+    # smartAnalysis
+    #
+    def smartAnalysis(self,analysis=None):
+        """
+        Main core function to compute INERT  on current snapshot stored in data_analysis
+        """
+        if analysis is None:
+            data=self.__analysis
+        else:
+            data=analysis
+        t0 = time.clock()
+        uns_snap=data.uns_snap # link to UNS object
+
+        ok,self.__time=uns_snap.getData("time")
+        print("Time =",self.__time)
+        
+        t_file=self.__inert_dir+"/.time_completed"
+
+        if not self.__checkTimeExist(self.__time,t_file): # time not computed yet
+
+            self.__openOutFile() # open file
+
+            self.__fdesc.write("%e\n"%(self.__time)) # save time
+            
+            # read data
+            ok,pos  = uns_snap.getData(self.__component,"pos")
+            if not ok:
+                raise Exception("No Positions particles for component <%s>...\n"%(self.__component))
+            ok,mass = uns_snap.getData(self.__component,"mass")
+            if not ok:
+                raise Exception("No Masses particles for component <%s>...\n"%(self.__component))
+
+            if self.__vdebug:
+                print("1:",pos)
+            # centering
+            ok=uns_snap.centerOnFile(pos,None,mass,self.__com,self.__component,self.__center_file,data)
+            if self.__vdebug:
+                print("2:",pos,ok)
+
+            # compute density
+            t00=time.clock()
+            if self.__tree_density:
+                ctree=CTree(pos,None,mass)  # instantiate a ctree object
+
+                cxv=ctree.fastCod3(self.__tree_threshold)
+                rho,hsml=ctree.getTreeDensity()
+                pos,vel,mass=ctree.getTreePart()
+            else : # full density
+                c=CFalcon() # new falcon object
+                ok,rho,hsml=c.getDensity(pos,mass) # compute density
+                pos=pos
+                mass=mass
+            print("Computing density : %.02f"%(time.clock()-t00),file=sys.stderr)    
+                
+            #embed()
+
+            pos=np.reshape(pos,(-1,3))        # pos reshaped in a 2D array [nbody,3]
+            #radius=np.sqrt(pos[:,0]*pos[:,0]+pos[:,1]*pos[:,1]+pos[:,2]*pos[:,2])  # compute particles radius
+            #rs = radius.argsort() # sort particles according their radius
+
+            sort_rho=(-rho).argsort() # sort according to higher density
+
+            nreal   = pos.size/3 # number total particles
+            npart   = (self.__fract_max-self.__fract_min)*nreal #   min<#particles<max
+            iinf    = nreal*self.__fract_min
+            offset  = iinf
+            imax    = nreal*self.__fract_max-1
+            step    = npart/self.__ncut   # #particles/step
+
+            print("range = <%d> [%d:%d] %d\n"%(nreal,iinf,imax,step))
+
+            # CALL SNAPINERT from iinf:imax 
+            #
+            #
+            ppos = pos [sort_rho[iinf:imax+1] , : ]
+            pmass= mass[sort_rho[iinf:imax+1]     ]
+            #embed()
+            mofi,U,s,rot = self.momentInertia(ppos,pmass)
+
+            # save on file
+            #self.__fdesc.write("%f "%(self.__time))        
+            if not self.__nonemo:
+                self.__saveData(mofi,U,s,rot)
+
+            stop=False
+            cpt=0
+            tot=step  # #particles cutted
+
+            sup = step
+            while not stop:
+                ifirst = iinf+step*cpt
+                ilast  = ifirst+step-1
+
+                if ilast>imax or cpt>self.__ncut:
+                    stop=True
+                    ilast=imax
+                
+                if ifirst< imax:
+                    ppos =pos [sort_rho[ifirst:ilast+1] , : ]
+                    pmass=mass[sort_rho[ifirst:ilast+1]     ]
+                    radius=np.sqrt(ppos[:,0]*ppos[:,0]+ppos[:,1]*ppos[:,1]+ppos[:,2]*ppos[:,2])  # compute particles radius
+                    rs=radius.argsort()
+                    print("<%07d,%07d> radius [%f,%f]"%(ifirst,ilast,
+                                                        radius[rs[0]],
+                                                        radius[rs[-1]]),
+                                                        file=sys.stderr)
+
+                    #embed()
+                    mofi,U,s,rot = self.momentInertia(ppos,pmass)
+
+                    # save on file
+                    self.__fdesc.write("%d %d\n"%(ifirst,ilast))
+                    if not self.__nonemo:
+                        self.__saveData(mofi,U,s,rot)
+                # 
+                cpt=cpt+1
+
+            self.__closeOutFile() # close file
+            self.__saveNewTime(self.__time,t_file) # save new time in ".time_completed" file
+        else:
+            print("INERT: skip time[%.3f] from <%s>\n"%(self.__time,t_file))
+
+
+    # 
+    # Inertia
+    #
+    def momentInertia(self,pos,weight):
+        """
+        compute Inertia moment based on 
+        https://scipython.com/blog/the-moment-of-inertia-of-a-random-flight-polymer/
+        """
+
+        # Calculate the moment of interia tensor
+        mofi = np.empty((3,3))
+        x, y, z = pos[:,0], pos[:,1], pos[:,2]
+
+        nemo=not self.__nonemo
+
+        if not nemo:
+            print("not Nemo method")
+            Ixx = np.sum((y**2 + z**2)*weight)
+            Iyy = np.sum((x**2 + z**2)*weight)
+            Izz = np.sum((x**2 + y**2)*weight)
+            Ixy = -np.sum(x * y * weight)
+            Iyz = -np.sum(y * z * weight)
+            Ixz = -np.sum(x * z * weight)
+        else:  # NEMO version based on snapinert
+            # modification regarding to snapinert.c   cf NEMO package
+            print("Nemo method")
+            Ixx = np.sum(x * x * weight)
+            Iyy = np.sum(y * y * weight)
+            Izz = np.sum(z * z * weight)
+            Ixy = np.sum(x * y * weight)
+            Iyz = np.sum(y * z * weight)
+            Ixz = np.sum(x * z * weight)
+
+
+        if nemo:
+            p_weight=np.sum(weight) # pos.size/3.
+        else:
+            p_weight=1.0
+
+        if self.__vdebug:
+            print("p_weight =",p_weight)
+                        
+
+        mofi = np.array(((Ixx/p_weight, Ixy/p_weight, Ixz/p_weight), 
+                         (Ixy/p_weight, Iyy/p_weight, Iyz/p_weight), 
+                         (Ixz/p_weight, Iyz/p_weight, Izz/p_weight)))
+
+        if self.__vdebug:
+            print("Inertia matrix:\n",mofi)
+
+        if nemo:
+            U, s, rot = linalg.svd(mofi)
+                
+            if self.__vdebug:        
+                print ("U=",U)
+                print ("s=",s)
+                print ("rot=",rot)
+                print ("s[1]/s[0]=",np.sqrt(s[1]/s[0]))
+                print ("s[2]/s[0]=",np.sqrt(s[2]/s[0]))
+
+            return mofi,U,s,rot
+
+        else : # nonemo (based on uns_shaperadius
+            eval,evec = linalg.eig(mofi)
+            idx=eval.argsort()[::]
+            eval=eval[idx]
+            evec=evec[:,idx]
+            print("Sorted")
+            print("eval =",eval)
+            print("evec =",evec)
+            hx=eval[0]
+            hy=eval[1]
+            hz=eval[2]
+            print("b/a=",np.sqrt((hx-hy+hz)/(-hx+hy+hz)))
+            print("c/a=",np.sqrt((hx+hy-hz)/(-hx+hy+hz)))
+            return 0,0,0,0
+        
+
+#            ,mofi[1,:],mofi[2,:])
+
+
+
+
+
+    # 
+    # save data
+    #
+    def __saveData(self,mofi,U,s,rot):
+
+        data=self.__analysis
+
+        # display on screen
+        if self.__vdebug:
+            print(self.__time,end="    ")
+            self.__fdesc.write("%f "%(self.__time))
+        for ii in range(0,3): # Ixx Ixy Ixz
+            if self.__vdebug:
+                print(mofi[0,ii],end="    ")
+            self.__fdesc.write("%f "%(mofi[0,ii]))
+
+        for ii in range(0,3): # Ixy Iyy Iyz
+            if self.__vdebug:
+                print(mofi[1,ii],end="    ")
+            self.__fdesc.write("%f "%(mofi[1,ii]))
+
+        for ii in range(0,3): # Ixz Iyz Izz 
+            if self.__vdebug:
+                print(mofi[2,ii],end="    ")
+            self.__fdesc.write("%f "%(mofi[2,ii]))
+
+        for ii in range(0,3): # s[0] s[1] s[2]
+            if self.__vdebug:
+                print(s[ii],end="    ")
+            self.__fdesc.write("%f "%(s[ii]))
+
+        for ii in range(0,3): # -rot[0.:]
+            if self.__vdebug:
+                print(rot[0,ii],end="    ")
+            self.__fdesc.write("%f "%(-rot[0,ii]))
+
+        for ii in range(0,3): # rot[1,:]
+            if self.__vdebug:
+                print(rot[1,ii],end="    ")
+            self.__fdesc.write("%f "%(rot[1,ii]))
+
+        for ii in range(0,3): # rot[2.:]
+            if self.__vdebug:
+                print(rot[2,ii],end="    ")
+            self.__fdesc.write("%f "%(rot[2,ii]))
+
+        print("\n")
+        self.__fdesc.write("\n")
+            
+            
+
+
+    #
+    # __openOutFile
+    #
+    def __openOutFile(self):
+        """
+        """
+        if hasattr(self.__analysis,"single_proc"): # full process analysis, file already open
+            return
+        else: # parallel analysis
+            #print(">>",self.__inert_dir)
+            #print(">>",self.__outfile_main)
+            #print(">>",self.__analysis.snap_id)
+            outfile= self.__inert_dir+"/.parallel/"+self.__outfile_main+".%05d"%(self.__analysis.snap_id)
+            self.__buildRes(outfile,self.simname)
+    #
+    # __closeOutFile
+    #
+    def __closeOutFile(self):
+        """
+        """
+        if hasattr(self.__analysis,"single_proc"): # full process analysis, file already open
+            return
+        else: # parallel analysis
+            self.__fdesc.close()
+
+    #
+    # __checkTimeExist
+    #
+    def __saveNewTime(self,time,t_file):
+        """
+        write in t_file a new time completed
+
+        *IN*
+        time    : current time
+        t_file  : filename
+    
+        """    
+        # lock process
+        self.__analysis.lock[self.__analysis.lock_id].acquire()
+        if self.__vdebug:
+            print("Saving a new INERT time[%.3f] in <%s>\n"%(time,t_file))
+        try:
+            f=open(t_file,"a")
+            f.write("%f\n"%(time))
+            f.close()
+        except:
+            print("\n\nUnable to save time[%.3f] in <%s>, aborting....\n"%(time,t_file))
+            sys.exit()
+        # release process
+        self.__analysis.lock[self.__analysis.lock_id].release()
+
+    #
+    # __checkTimeExist
+    #
+    def __checkTimeExist(self,time,t_file):
+        """
+        check in t_file, if time has been already computed
+
+        *IN*
+        time    : current time
+        t_file  : file with time value
+    
+        *OUT*
+        boolean : True if time exist, False otherwise        
+        
+        """
+        if os.path.isfile(t_file):
+            try:
+                f=open(t_file,"r")
+                while True:
+                    atime=map(np.float,(f.readline().split()))
+                    if (len(atime)>0):
+                        if (atime[0]-0.001)<time and (atime[0]+0.001)>time:
+                            f.close()
+                            return True
+                    else:
+                        f.close()
+                        return False
+
+            except EOFError:
+                pass
+        else:
+            if self.__vdebug:
+                print("FILE <%s> does not exist...\n"%(t_file))
+
+        return False

py/modules/simulations/cplotinert.py

+#!/usr/bin/python
+from __future__ import print_function
+from uns_simu import *
+
+import time
+import os,sys
+import numpy as np
+import math
+import time
+
+import matplotlib.pyplot as plt
+import matplotlib.gridspec as gridspec
+#from IPython import embed
+
+#
+