From 618f6b678a3782a43d8015350da01c5c73b8547d Mon Sep 17 00:00:00 2001 From: Ian Jauslin Date: Sat, 5 May 2018 23:18:02 +0000 Subject: Initial commit --- figs/atoms.fig/Makefile | 15 +++ figs/atoms.fig/chiral-base.gp | 22 +++++ figs/atoms.fig/chiral.py | 102 +++++++++++++++++++++ figs/atoms.fig/crystal-base.gp | 21 +++++ figs/atoms.fig/crystal.py | 26 ++++++ figs/atoms.fig/liquid-base.gp | 21 +++++ figs/atoms.fig/liquid.py | 39 ++++++++ figs/atoms.fig/nematic-base.gp | 21 +++++ figs/atoms.fig/nematic.py | 90 ++++++++++++++++++ figs/dimer_example.fig/Makefile | 32 +++++++ figs/dimer_example.fig/dimer_conf.py | 167 ++++++++++++++++++++++++++++++++++ figs/dimer_example.fig/libs/dimer.sty | 33 +++++++ figs/pyrite.jpg | Bin 0 -> 1174270 bytes 13 files changed, 589 insertions(+) create mode 100644 figs/atoms.fig/Makefile create mode 100644 figs/atoms.fig/chiral-base.gp create mode 100644 figs/atoms.fig/chiral.py create mode 100644 figs/atoms.fig/crystal-base.gp create mode 100644 figs/atoms.fig/crystal.py create mode 100644 figs/atoms.fig/liquid-base.gp create mode 100644 figs/atoms.fig/liquid.py create mode 100644 figs/atoms.fig/nematic-base.gp create mode 100644 figs/atoms.fig/nematic.py create mode 100644 figs/dimer_example.fig/Makefile create mode 100644 figs/dimer_example.fig/dimer_conf.py create mode 100644 figs/dimer_example.fig/libs/dimer.sty create mode 100644 figs/pyrite.jpg (limited to 'figs') diff --git a/figs/atoms.fig/Makefile b/figs/atoms.fig/Makefile new file mode 100644 index 0000000..2cffa07 --- /dev/null +++ b/figs/atoms.fig/Makefile @@ -0,0 +1,15 @@ +PROJECTNAME=nematic liquid crystal chiral +PNGS=$(addsuffix .png, $(PROJECTNAME)) + +all: $(PNGS) + +$(PNGS): + cp $(patsubst %.png, %, $@)-base.gp $(patsubst %.png, %, $@).gp + python $(patsubst %.png, %, $@).py >> $(patsubst %.png, %, $@).gp + gnuplot $(patsubst %.png, %, $@).gp > $@ + +clean-aux: + rm -f $(addsuffix .gp, $(PROJECTNAME)) + +clean: clean-aux + rm -f $(PNGS) diff --git a/figs/atoms.fig/chiral-base.gp b/figs/atoms.fig/chiral-base.gp new file mode 100644 index 0000000..5960ce6 --- /dev/null +++ b/figs/atoms.fig/chiral-base.gp @@ -0,0 +1,22 @@ +set terminal pngcairo size 2048,2048 + +set key off +unset colorbox +unset border +unset xtics +unset ytics +unset ztics + +set parametric + +set view 80,10,1.5 +set view equal xyz + +set isosample 100 + +set pm3d depthorder +set pm3d lighting primary 0.50 specular 0.6 + +set palette defined (0 "#339999", 1 "#339999") + +splot \ diff --git a/figs/atoms.fig/chiral.py b/figs/atoms.fig/chiral.py new file mode 100644 index 0000000..eed6df8 --- /dev/null +++ b/figs/atoms.fig/chiral.py @@ -0,0 +1,102 @@ +#!/usr/bin/env python3 + +from math import * +import random +import sys + +# size of space +L=30 +# number of lines +H=5 +# heigh of lines +height=5 +# number of rods per line +N=16 +# aspect ratio +a=10 +# spread in theta angle +spread_t=pi/60 +# in phi +spread_p=pi/60 +# in height +spread_h=1/120 + +# check whether two rods overlap +def check_overlap(rod1,rod2): + # relative placement + relative_pos=unrotate(subtract(rod2[0],rod1[0]), rod1[1]) + if(abs(relative_pos[0])<2 and abs(relative_pos[1])<2 and abs(relative_pos[2])<2): + return(True) + # relative angle + relative_ang=cart_to_spherical(unrotate(spherical_to_cart(rod2[1]), rod1[1])) + # exclusion volume + # rotate other rod + relative_pos=unrotate(relative_pos, [0,relative_ang[1]]) + #if(abs(relative_pos[1])<2 and abs(relative_pos[0])-21 and abs(c)<1.0001): + if(c>0): + return([w[0],0]) + else: + return([w[0],pi]) + if(s>=0): + return([w[0],acos(c)]) + return([w[0],2*pi-acos(c)]) + +# configuration +config=[] +# add rods +for h in range(H): + config_h=[] + while len(config_h)1 and abs(c)<1.0001): + if(c>0): + return([w[0],0]) + else: + return([w[0],pi]) + if(s>=0): + return([w[0],acos(c)]) + return([w[0],2*pi-acos(c)]) + +# configuration +config=[] +# add rods +while len(config)=L or e[1]+d[1]>=L or mask[e[0]][e[1]]==0 or mask[e[0]+d[0]][e[1]+d[1]]==0): + e=[random.randint(0,L-1),random.randint(0,L-1)] + # check whether a dimer can be added to the edge + if(occupied[e[0]][e[1]]==0 and occupied[e[0]+d[0]][e[1]+d[1]]==0): + # number of interactions + interactions=0 + if(e[0]+2*d[0]=0 and e[1]-d[1]>=0 and occupied[e[0]-d[0]][e[1]-d[1]]==1): + interactions=interactions+1 + # probability of adding the dimer + p=1/(1+1/z*exp(-J*interactions)) + if(p>random.random()): + # add dimer + dimers.append(e) + occupied[e[0]][e[1]]=1 + occupied[e[0]+d[0]][e[1]+d[1]]=1 + + return(dimers) + +# find interactions +def interactions(dimers,direction): + if(direction=="h"): + d=[1,0] + else: + d=[0,1] + + out=[] + for d1 in dimers: + for d2 in dimers: + if(d1[0]-d2[0]==2*d[0] and d1[1]-d2[1]==2*d[1]): + out.append([d2[0]+d[0],d2[1]+d[1]]) + return(out) + + +# draw dimers +def draw_dimers(v_dimers,h_dimers,file_desc,color): + for d in v_dimers: + print("\\dimer{[color="+color+"]("+str(d[0])+","+str(d[1])+")}v", file=file_desc) + print("", file=file_desc) + for d in h_dimers: + print("\\dimer{[color="+color+"]("+str(d[0])+","+str(d[1])+")}h", file=file_desc) + print("", file=file_desc) + +# draw interactions +def draw_interactions(v_interactions,h_interactions,file_desc): + for d in v_interactions: + print("\\interaction{("+str(d[0])+","+str(d[1])+")}v", file=file_desc) + print("", file=file_desc) + for d in h_interactions: + print("\\interaction{("+str(d[0])+","+str(d[1])+")}h", file=file_desc) + print("", file=file_desc) + +# init tikz file +def init_tikz(filename): + file_desc=open(filename,"w") + print("\\documentclass{standalone}\n\n\\usepackage{tikz}\n\\usepackage{dimer}\n\\usetikzlibrary{decorations.pathmorphing}\n\n\\begin{document}\n\\begin{tikzpicture}\n\n", file=file_desc) + return(file_desc) + +# close tikz file +def close_tikz(file_desc): + print("\\end{tikzpicture}\n\\end{document}", file=file_desc) + file_desc.close() + +mu=int(L/2) + + +# masks +# init +v_mask=[] +h_mask=[] +for i in range(L): + v_mask.append([]) + h_mask.append([]) + for j in range(L): + v_mask[i].append(1) + h_mask[i].append(0) +# draw masks +for i in range(mu-l0,mu+l0): + for j in range(mu+1,mu+5): + v_mask[i][j]=0 +for i in range(mu-2*l0,mu+2*l0): + for j in range(mu-5,mu+1): + v_mask[i][j]=0 +for i in range(mu-l0+2,mu+l0-2): + for j in range(mu+1,mu+4): + h_mask[i][j]=1 +for i in range(mu-l0,mu+l0): + h_mask[i][mu]=1 +for i in range(mu-2*l0+2,mu+2*l0-2): + for j in range(mu-4,mu): + h_mask[i][j]=1 +h_mask[mu-1][mu+1]=0 +h_mask[mu-1][mu+2]=0 +h_mask[mu-1][mu-3]=0 +h_mask[mu-1][mu-2]=0 +h_mask[mu][mu-3]=0 +h_mask[mu][mu-2]=0 + +# random dimers in mask +v_dimers=fill_dimers(v_mask,"v") +h_dimers=fill_dimers(h_mask,"h") + +# mantle dimers +h_mantle=[] +for i in range(0,l0): + h_mantle.append([mu-l0+2*i,mu+4]) +for i in range(0,4): + h_mantle.append([mu+l0-2,mu+4-i]) + h_mantle.append([mu-l0,mu+4-i]) +for i in range(0,int(l0/2)): + h_mantle.append([mu+l0+2*i,mu]) + h_mantle.append([mu-l0-2-2*i,mu]) +for i in range(0,5): + h_mantle.append([mu+2*l0-2,mu-i]) + h_mantle.append([mu-2*l0,mu-i]) +for i in range(0,2*l0): + h_mantle.append([mu-2*l0+2*i,mu-5]) + +v_mantle=[] +v_mantle.append([mu-1,mu+1]) +v_mantle.append([mu-1,mu-3]) +v_mantle.append([mu,mu-3]) + +# interactions +v_interactions=interactions(v_dimers+v_mantle,"v") +h_interactions=interactions(h_dimers+h_mantle,"h") + +# files +interaction=init_tikz("interaction.tikz.tex") +print("\\grid{"+str(L-1)+"}{"+str(L-1)+"}{(0,0)}\n", file=interaction) +draw_interactions(v_interactions,h_interactions,interaction) +draw_dimers(v_dimers+v_mantle,h_dimers+h_mantle,interaction,"black") +close_tikz(interaction) diff --git a/figs/dimer_example.fig/libs/dimer.sty b/figs/dimer_example.fig/libs/dimer.sty new file mode 100644 index 0000000..0f087ef --- /dev/null +++ b/figs/dimer_example.fig/libs/dimer.sty @@ -0,0 +1,33 @@ +% square lattice (width #1, height #2, origin #3) +\def\grid#1#2#3{ + \foreach\i in {0,...,#2}{ + \draw#3++(0,\i)--++(#1,0); + } + \foreach\i in {0,...,#1}{ + \draw#3++(\i,0)--++(0,#2); + } +} + +% dimer (bottom-left vertex #1, vertical or horizontal #2) +\def\dimer#1#2{ + \if#2h + \draw[line width=5pt]#1--++(1,0); + \fill#1circle(7pt); + \fill#1++(1,0)circle(7pt); + \else + \draw[line width=5pt]#1--++(0,1); + \fill#1circle(7pt); + \fill#1++(0,1)circle(7pt); + \fi +} + +% interactions (bottom-left vertex #1, vertical or horizontal #2) +\def\interaction#1#2{ + \if#2h + \draw[line width=5pt, color=white]#1--++(1,0); + \draw[line width=4pt, decorate, decoration={snake}, color=red]#1--++(1,0); + \else + \draw[line width=5pt, color=white]#1--++(0,1); + \draw[line width=4pt, decorate, decoration={snake}, color=red]#1--++(0,1); + \fi +} diff --git a/figs/pyrite.jpg b/figs/pyrite.jpg new file mode 100644 index 0000000..59a9ae5 Binary files /dev/null and b/figs/pyrite.jpg differ -- cgit v1.2.3-70-g09d2