Commit b7378502 authored by Germain Clavier's avatar Germain Clavier
Browse files

Several modifications to the following files to make the new examples work. 

Plotview is annoying. Duck it. Duck all visualisation libs form this repo.
parent 4809ebef

examples/test_animate.py

+3 −1
Original line number Diff line number Diff line 
# simple test of animate tool

# requires files/bucky*png files



import animate



a = animate("files/bucky*gif")

a.play()

a.delay(0.1)
@@ -11,4 +13,4 @@ a.next() 
a.previous()

a.frame(1)



print "all done ... type CTRL-D to exit Pizza.py"
 
print("all done ... type CTRL-D to exit Pizza.py")

src/animate.py

+13 −11
Original line number Diff line number Diff line
@@ -67,9 +67,9 @@ class animate: 


        # convert filestr into full list of files



        list = str.split(filestr)

        files = str.split(filestr)

        self.files = []

        for file in list:

        for file in files:

            self.files += glob.glob(file)

        self.nframes = len(self.files)

        if self.nframes == 0:
@@ -79,22 +79,20 @@ class animate: 


        # load all images



        tkroot = Tk()

        self.tkroot = tkroot



        win1 = Toplevel(tkroot)

        win1.title("Pizza.py animate tool")



        self.images = []

        for i in range(self.nframes):

            self.images.append(PhotoImage(file=self.files[i]))



        # grab Tk instance from main



        # from __main__ import tkroot



        tkroot = Tk()

        self.tkroot = tkroot



        # GUI control window



        win1 = Toplevel(tkroot)

        win1.title("Pizza.py animate tool")



        holder1 = Frame(win1)

        button1 = Button(holder1, text="<<", command=self.first).pack(side=LEFT)

        button2 = Button(holder1, text="<", command=self.previous).pack(side=LEFT)
@@ -137,13 +135,17 @@ class animate: 
        win2 = Toplevel(tkroot)

        self.image_pane = Label(win2, image=self.images[0])

        self.image_pane.pack(side=BOTTOM)

        tkroot.update_idletasks()  # force window to appear

        self.tkroot.update_idletasks()  # force window to appear



        # display 1st image



        self.index = 0

        self.display(self.index)



        # More comfortable to have a small delay IMO

        self.delay(0.1)

        self.tkroot.mainloop()



    # --------------------------------------------------------------------



    def first(self):

src/cdata.py

+50 −24
Original line number Diff line number Diff line
@@ -160,6 +160,7 @@ import sys 
import glob

from os import popen

from math import sqrt, pi, cos, sin, fabs

import numpy as np

from copy import deepcopy



try:
@@ -547,29 +548,39 @@ class cdata: 


        cmd1 = teststr.replace("$x", "o.vertices[v1][0]")

        cmd1 = cmd1.replace("$y", "o.vertices[v1][1]")

        cmd1 = "flag1 = " + cmd1.replace("$z", "o.vertices[v1][2]")

        ccmd1 = compile(cmd1, "", "single")

        # cmd1 = "flag1 = " + cmd1.replace("$z", "o.vertices[v1][2]")

        cmd1 = cmd1.replace("$z", "o.vertices[v1][2]")

        # ccmd1 = compile(cmd1, "", "single")



        cmd2 = teststr.replace("$x", "o.vertices[v2][0]")

        cmd2 = cmd2.replace("$y", "o.vertices[v2][1]")

        cmd2 = "flag2 = " + cmd2.replace("$z", "o.vertices[v2][2]")

        ccmd2 = compile(cmd2, "", "single")

        # cmd2 = "flag2 = " + cmd2.replace("$z", "o.vertices[v2][2]")

        cmd2 = cmd2.replace("$z", "o.vertices[v2][2]")

        # ccmd2 = compile(cmd2, "", "single")



        cmd3 = teststr.replace("$x", "o.vertices[v3][0]")

        cmd3 = cmd3.replace("$y", "o.vertices[v3][1]")

        cmd3 = "flag3 = " + cmd3.replace("$z", "o.vertices[v3][2]")

        ccmd3 = compile(cmd3, "", "single")

        # cmd3 = "flag3 = " + cmd3.replace("$z", "o.vertices[v3][2]")

        cmd3 = cmd3.replace("$z", "o.vertices[v3][2]")

        # ccmd3 = compile(cmd3, "", "single")

        print(cmd1)

        print(cmd2)

        print(cmd3)



        # loop over triangles in id_surf

        # 3 vertices must satisfy all 3 tests for tri's inclusion in new surf obj

        # 3 vertices must satisfy all 3 tests

        # for tri's inclusion in new surf obj



        for tri in o.triangles:

            v1 = tri[0] - 1

            v2 = tri[1] - 1

            v3 = tri[2] - 1

            exec(ccmd1)

            exec(ccmd2)

            exec(ccmd3)

            # flag1 = o.vertices[v1][2] < 2.0

            # flag2 = o.vertices[v2][2] < 2.0

            # flag3 = o.vertices[v3][2] < 2.0

            flag1 = eval(cmd1)

            flag2 = eval(cmd2)

            flag3 = eval(cmd3)

            # Flags defined in commands

            if flag1 and flag2 and flag3:

                obj.vertices.append(o.vertices[v1][:])
@@ -616,7 +627,8 @@ class cdata: 
        if out_id:

            out_obj = self.objs[self.ids[out_id]]



        # pre-process SURFACE objects to bin their triangles for faster searching

        # pre-process SURFACE objects to bin

        # their triangles for faster searching



        if in_obj.style == SURFACE:

            in_obj.inside_prep()
@@ -629,15 +641,23 @@ class cdata: 
        xsize = xhi - xlo

        ysize = yhi - ylo

        zsize = zhi - zlo

        print("bbox:")

        print(xlo, xhi, xsize)

        print(ylo, yhi, ysize)

        print(zlo, zhi, zsize)



        # generate particles until have enough that satisfy in/out constraints



        count = attempt = 0

        while count < npart:

            attempt += 1

            x = xlo + self.random() * xsize

            y = ylo + self.random() * ysize

            z = zlo + self.random() * zsize

            x = xlo + np.random.random() * xsize

            y = ylo + np.random.random() * ysize

            z = zlo + np.random.random() * zsize

            # x = xlo + self.random() * xsize

            # y = ylo + self.random() * ysize

            # z = zlo + self.random() * zsize

            # print(x, y, z)

            if not in_obj.inside(x, y, z):

                continue

            if out_id and out_obj.inside(x, y, z):
@@ -666,7 +686,9 @@ class cdata: 
        obj.xyz = []



        on_obj = self.objs[self.ids[on_id]]

        if on_obj.style != SURFACE and on_obj.style != REGION and on_obj.style != UNION:

        if (on_obj.style != SURFACE

           and on_obj.style != REGION

           and on_obj.style != UNION):

            sys.exit("Illegal ID to place particles on")

        totalarea = on_obj.area()
@@ -1478,7 +1500,8 @@ class Surface: 
    # project 3d triangles to xy plane

    # only need examine triangles in bin that point is in

    # if pt is outside bins, don't need to check

    # x,y,z is inside surf if line segment intersects an odd number of triangles

    # x,y,z is inside surf if line segment intersects

    # an odd number of triangles

    # intersection test:

    #   is xy pt in bounding rectangle of tri in xy plane ?

    #   is xy pt inside tri in xy plane (including edges and vertices) ?
@@ -1488,6 +1511,7 @@ class Surface: 
    def inside(self, x, y, z):

        ix = int((x - self.xlo) * self.dxinv)

        iy = int((y - self.ylo) * self.dyinv)

        print(ix, self.nbinx, iy, self.nbiny)

        if ix < 0 or ix >= self.nbinx or iy < 0 or iy >= self.nbiny:

            return 0

        n = len(self.bin[ix][iy])
@@ -1513,7 +1537,8 @@ class Surface: 
                continue



            # is x,y inside 2d triangle ?

            # cross product of each edge with vertex-to-point must have same sign

            # cross product of each edge

            # with vertex-to-point must have same sign

            # cross product = 0 is OK, means point is on edge or vertex



            c1 = (v2[0]-v1[0]) * (y-v1[1]) - (v2[1]-v1[1]) * (x-v1[0])
@@ -1535,7 +1560,8 @@ class Surface: 
            # p = (x,y) - v1, v = v2 - v1, w = v3 - v2

            # find alpha,beta such that p = alpha v + beta w

            # by solving system of 2 linear eqs for their intersection

            # denom (vx - vy * wx/xy) cannot be 0 since would imply vx/vy = wx/wy

            # denom (vx - vy * wx/xy) cannot be 0

            # since would imply vx/vy = wx/wy

            # and thus e1 would be parallel to e2

            # if wy = 0, vy cannot be 0, since e1 would be parallel to e2

src/chain.py

+29 −17
Original line number Diff line number Diff line
@@ -54,6 +54,7 @@ c.write("data.file") write out all built chains to LAMMPS data file 


import math

import sys

import numpy as np

from data import data



# Class definition
@@ -74,6 +75,7 @@ class chain: 
        self.seed = 12345

        self.mtype = 1

        self.btype = 1

        self.charge = 0.

        self.blen = 0.97

        self.dmin = 1.02

        self.id = "chain"
@@ -92,7 +94,9 @@ class chain: 
        self.zlo = -self.zprd / 2.0

        self.zhi = self.zprd / 2.0



        print("Simulation box: %g by %g by %g" % (self.xprd, self.yprd, self.zprd))

        print("Simulation box: %g by %g by %g" %

              (self.xprd, self.yprd, self.zprd)

              )



    # --------------------------------------------------------------------
@@ -101,26 +105,29 @@ class chain: 
            atoms = []

            bonds = []

            id_atom_prev = id_mol_prev = id_bond_prev = 0

            if len(self.atoms):

            if self.atoms:

                id_atom_prev = self.atoms[-1][0]

                id_mol_prev = self.atoms[-1][1]

            if len(self.bonds):

            if self.bonds:

                id_bond_prev = self.bonds[-1][0]



            for imonomer in range(nper):

                if imonomer == 0:

                    x = self.xlo + self.random() * self.xprd

                    y = self.ylo + self.random() * self.yprd

                    z = self.zlo + self.random() * self.zprd

                    # x = self.xlo + self.random() * self.xprd

                    # y = self.ylo + self.random() * self.yprd

                    # z = self.zlo + self.random() * self.zprd

                    x = np.random.uniform(self.xlo, self.xhi)

                    y = np.random.uniform(self.xlo, self.xhi)

                    z = np.random.uniform(self.xlo, self.xhi)

                    ix = iy = iz = 0

                else:

                    restriction = True

                    while restriction:

                        rsq = 2.0

                        while rsq > 1.0:

                            dx = 2.0 * self.random() - 1.0

                            dy = 2.0 * self.random() - 1.0

                            dz = 2.0 * self.random() - 1.0

                            dx = np.random.uniform(-1, 1)

                            dy = np.random.uniform(-1, 1)

                            dz = np.random.uniform(-1, 1)

                            rsq = dx * dx + dy * dy + dz * dz

                        r = math.sqrt(rsq)

                        dx, dy, dz = dx / r, dy / r, dz / r
@@ -148,7 +155,11 @@ class chain: 
                else:

                    sys.exit("chain ID is not a valid value")



                atoms.append([idatom, idmol, self.mtype, x, y, z, ix, iy, iz])

                atcharge = self.charge

                atoms.append(

                        [idatom, idmol, self.mtype, atcharge,

                         x, y, z, ix, iy, iz]

                        )

                if imonomer:

                    bondid = id_bond_prev + imonomer

                    bonds.append([bondid, self.btype, idatom - 1, idatom])
@@ -188,12 +199,12 @@ class chain: 


        lines = []

        for i in range(atypes):

            lines.append("%d 1.0\n" % (i + 1))

            lines.append("%d 1.0" % (i + 1))

        d.sections["Masses"] = lines



        lines = []

        for atom in self.atoms:

            line = "%d %d %d %g %g %g %d %d %d\n" % (

            line = "{:>} {:>} {:>} {:>} {:>} {:>} {:>} {:>} {:>} {:>}".format(

                atom[0],

                atom[1],

                atom[2],
@@ -203,13 +214,14 @@ class chain: 
                atom[6],

                atom[7],

                atom[8],

                atom[9]

            )

            lines.append(line)

        d.sections["Atoms"] = lines



        lines = []

        for bond in self.bonds:

            line = "%d %d %d %d\n" % (bond[0], bond[1], bond[2], bond[3])

            line = "%d %d %d %d" % (bond[0], bond[1], bond[2], bond[3])

            lines.append(line)

        d.sections["Bonds"] = lines

src/data.py

+2 −1
Original line number Diff line number Diff line
@@ -277,11 +277,12 @@ class data: 
                        )

                    )

                else:

                    f.write("{}\n".format(self.headers[keyword], keyword))

                    f.write("{} {}\n".format(self.headers[keyword], keyword))

        for pair in skeywords:

            keyword = pair[0]

            if keyword in self.sections:

                f.write("\n%s\n" % keyword)

                f.write("\n")

                for line in self.sections[keyword]:

                    f.write("{}\n".format(line))

        f.close()