/usr/share/pyshared/ase/gui/execute.py is in python-ase 3.6.0.2515-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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import __future__
import gtk
from gettext import gettext as _
import os.path
import numpy as np
import sys
from ase.gui.widgets import pack, Help
from ase.data.colors import jmol_colors
from ase.atoms import Atoms
class Execute(gtk.Window):
""" The Execute class provides an expert-user window for modification
and evaluation of system properties with a simple one-line command structure.
There are two types of commands, one set only applies to the global image and
one set applies to all atoms. If the command line contains any of the atom
commands, then it is executed separately for all atoms and for all images.
Otherwise it is executed only once per image.
Please do not mix global and atom commands."""
terminal_help_txt=_("""
Global commands work on all frames or only on the current frame
- Assignment of a global variable may not reference a local one
- use 'Current frame' switch to switch off application to all frames
<c>e</c>:\t\ttotal energy of one frame
<c>fmax</c>:\tmaximal force in one frame
<c>A</c>:\tunit cell
<c>E</c>:\t\ttotal energy array of all frames
<c>F</c>:\t\tall forces in one frame
<c>M</c>:\tall magnetic moments
<c>R</c>:\t\tall atomic positions
<c>S</c>:\tall selected atoms (boolean array)
<c>D</c>:\tall dynamic atoms (boolean array)
examples: <c>frame = 1</c>, <c>A[0][1] += 4</c>, <c>e-E[-1]</c>
Atom commands work on each atom (or a selection) individually
- these can use global commands on the RHS of an equation
- use 'selected atoms only' to restrict application of command
<c>x,y,z</c>:\tatomic coordinates
<c>r,g,b</c>:\tatom display color, range is [0..1]
<c>rad</c>:\tatomic radius for display
<c>s</c>:\t\tatom is selected
<c>d</c>:\t\tatom is movable
<c>f</c>:\t\tforce
<c>Z</c>:\tatomic number
<c>m</c>:\tmagnetic moment
examples: <c>x -= A[0][0], s = z > 5, Z = 6</c>
Special commands and objects:
<c>sa,cf</c>:\t(un)restrict to selected atoms/current frame
<c>frame</c>:\tframe number
<c>center</c>:\tcenters the system in its existing unit cell
<c>del S</c>:\tdelete selection
<c>CM</c>:\tcenter of mass
<c>ans[-i]</c>:\tith last calculated result
<c>exec file</c>: executes commands listed in file
<c>cov[Z]</c>:(read only): covalent radius of atomic number Z
<c>gui</c>:\tadvanced: ag window python object
<c>img</c>:\tadvanced: ag images object
""")
def __init__(self, gui):
gtk.Window.__init__(self)
self.gui = gui
self.set_title(_('Expert user mode'))
vbox = gtk.VBox()
vbox.set_border_width(5)
self.sw = gtk.ScrolledWindow()
self.sw.set_policy(gtk.POLICY_AUTOMATIC, gtk.POLICY_AUTOMATIC)
self.textview = gtk.TextView()
self.textbuffer = self.textview.get_buffer()
self.textview.set_editable(False)
self.textview.set_cursor_visible(False)
self.sw.add(self.textview)
pack(vbox, self.sw, expand=True, padding = 5)
self.sw.set_size_request(540, 150)
self.textview.show()
self.add_text(_('Welcome to the ASE Expert user mode'))
self.cmd = gtk.Entry(60)
self.cmd.connect('activate', self.execute)
self.cmd.connect('key-press-event', self.update_command_buffer)
pack(vbox, [gtk.Label('>>>'),self.cmd])
self.cmd_buffer = getattr(gui,'expert_mode_buffer',[''])
self.cmd_position = len(self.cmd_buffer)-1
self.selected = gtk.CheckButton(_('Only selected atoms (sa) '))
self.selected.connect('toggled',self.selected_changed)
self.images_only = gtk.CheckButton(_('Only current frame (cf) '))
self.images_only.connect('toggled',self.images_changed)
pack(vbox, [self.selected, self.images_only])
save_button = gtk.Button(stock=gtk.STOCK_SAVE)
save_button.connect('clicked',self.save_output)
help_button = gtk.Button(stock=gtk.STOCK_HELP)
help_button.connect('clicked',self.terminal_help,"")
stop_button = gtk.Button(stock=gtk.STOCK_STOP)
stop_button.connect('clicked',self.stop_execution)
self.stop = False
pack(vbox, [gtk.Label(_('Global: Use A, D, E, M, N, R, S, n, frame;'
' Atoms: Use a, f, m, s, x, y, z, Z ')),
stop_button, help_button, save_button], end = True)
self.add(vbox)
vbox.show()
self.show()
# set color mode to manual when opening this window for rgb manipulation
self.colors = self.gui.get_colors()
rgb_data = self.gui.get_colors(rgb = True)
self.rgb_data = [] # ensure proper format of rgb_data
for i, rgb in enumerate(rgb_data):
self.rgb_data += [[i, rgb]]
self.gui.colordata = self.rgb_data
self.gui.colors = list(self.colors)
self.gui.colormode = 'manual'
self.cmd.grab_focus()
def execute(self, widget=None, cmd = None):
global_commands = ['A','Col','D','e','E','F','frame','M','n','N','R','S'] # explicitly 'implemented' commands for use on whole system or entire single frame
index_commands = ['a','b','d','f','g','m','r','rad','s','x','y','z','Z'] # commands for use on all (possibly selected) atoms
new = self.gui.drawing_area.window.new_gc
alloc = self.gui.colormap.alloc_color
self.stop = False
if cmd is None:
cmd = self.cmd.get_text().strip()
if len(cmd) == 0:
return
self.add_text('>>> '+cmd)
self.cmd_buffer[-1] = cmd
self.cmd_buffer += ['']
setattr(self.gui,'expert_mode_buffer', self.cmd_buffer)
self.cmd_position = len(self.cmd_buffer)-1
self.cmd.set_text('')
else:
self.add_text('--> '+cmd)
gui = self.gui
img = gui.images
frame = gui.frame
N = img.nimages
n = img.natoms
S = img.selected
D = img.dynamic[:, np.newaxis]
E = img.E
if self.selected.get_active():
indices = np.where(S)[0]
else:
indices = range(n)
ans = getattr(gui,'expert_mode_answers',[])
loop_images = range(N)
if self.images_only.get_active():
loop_images = [self.gui.frame]
# split off the first valid command in cmd to determine whether
# it is global or index based, this includes things such as 4*z and z*4
index_based = False
first_command = cmd.split()[0]
special = ['=',',','+','-','/','*',';','.','[',']','(',')',
'{','}','0','1','2','3','4','5','6','7','8','9']
while first_command[0] in special and len(first_command)>1:
first_command = first_command[1:]
for c in special:
if c in first_command:
first_command = first_command[:first_command.find(c)]
for c in index_commands:
if c == first_command:
index_based = True
name = os.path.expanduser('~/.ase/'+cmd)
# check various special commands:
if os.path.exists(name): # run script from default directory
self.run_script(name)
elif cmd == 'del S': # delete selection
gui.delete_selected_atoms()
elif cmd == 'sa': # selected atoms only
self.selected.set_active(not self.selected.get_active())
elif cmd == 'cf': # current frame only
self.images_only.set_active(not self.images_only.get_active())
elif cmd == 'center': # center system
img.center()
elif cmd == 'CM': # calculate center of mass
for i in loop_images:
if self.stop:
break
atoms = Atoms(positions=img.P[i][indices],
numbers=img.Z[indices])
self.add_text(repr(atoms.get_center_of_mass()))
ans += [atoms.get_center_of_mass()]
elif first_command == 'exec': # execute script
name = cmd.split()[1]
if '~' in name:
name = os.path.expanduser(name)
if os.path.exists(name):
self.run_script(name)
else:
self.add_text(_('*** WARNING: file does not exist - %s') % name)
else:
code = compile(cmd + '\n', 'execute.py', 'single',
__future__.CO_FUTURE_DIVISION)
if index_based and len(indices) == 0 and self.selected.get_active():
self.add_text(_("*** WARNING: No atoms selected to work with"))
for i in loop_images:
if self.stop:
break
R = img.P[i][indices]
A = img.A[i]
F = img.F[i][indices]
e = img.E[i]
M = img.M[i][indices]
Col = []
cov = img.covalent_radii
for j in indices:
Col += [gui.colordata[j]]
if len(indices) > 0:
fmax = max(((F * D[indices])**2).sum(1)**.5)
else:
fmax = None
frame = gui.frame
if not index_based:
try:
self.add_text(repr(eval(cmd)))
ans += [eval(cmd)]
except:
exec code
gui.set_frame(frame)
if gui.movie_window is not None:
gui.movie_window.frame_number.value = frame
img.selected = S
img.A[i] = A
img.P[i][indices] = R
img.M[i][indices] = M
else:
for n,a in enumerate(indices):
if self.stop:
break
x, y, z = R[n]
r, g, b = Col[n][1]
d = D[a]
f = np.vdot(F[n]*d,F[n]*d)**0.5
s = S[a]
Z = img.Z[a]
Zold = Z
m = M[n]
rad = img.r[a]
try:
self.add_text(repr(eval(cmd)))
ans += [eval(cmd)]
except:
exec code
S[a] = s
img.P[i][a] = x, y, z
img.Z[a] = Z
img.r[a] = rad
img.dynamic[a] = d
if Z != Zold:
img.r[a] = cov[Z] * 0.89
r,g,b = jmol_colors[Z]
gui.colordata[a] = [a,[r,g,b]]
color = tuple([int(65535*x) for x in [r,g,b]])
gui.colors[a] = new(alloc(*color))
img.M[i][a] = m
setattr(self.gui,'expert_mode_answers', ans)
gui.set_frame(frame,init=True)
def add_text(self,val):
text_end = self.textbuffer.get_end_iter()
self.textbuffer.insert(text_end,val+'\n');
if self.sw.get_vscrollbar() is not None:
scroll = self.sw.get_vscrollbar().get_adjustment()
scroll.set_value(scroll.get_upper())
def selected_changed(self, *args):
if self.selected.get_active():
self.add_text(_('*** Only working on selected atoms'))
else:
self.add_text(_('*** Working on all atoms'))
def images_changed(self, *args):
if self.images_only.get_active():
self.add_text(_('*** Only working on current image'))
else:
self.add_text(_('*** Working on all images'))
def update_command_buffer(self, entry, event, *args):
arrow = {gtk.keysyms.Up: -1, gtk.keysyms.Down: 1}.get(event.keyval, None)
if arrow is not None:
self.cmd_position += arrow
self.cmd_position = max(self.cmd_position,0)
self.cmd_position = min(self.cmd_position,len(self.cmd_buffer)-1)
cmd = self.cmd_buffer[self.cmd_position]
self.cmd.set_text(cmd)
return True
else:
return False
def save_output(self, *args):
chooser = gtk.FileChooserDialog(
_('Save Terminal text ...'), None, gtk.FILE_CHOOSER_ACTION_SAVE,
(gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL,
gtk.STOCK_SAVE, gtk.RESPONSE_OK))
save = chooser.run()
if save == gtk.RESPONSE_OK or save == gtk.RESPONSE_SAVE:
filename = chooser.get_filename()
text = self.textbuffer.get_text(self.textbuffer.get_start_iter(),
self.textbuffer.get_end_iter())
fd = open(filename,'w')
fd.write(text)
fd.close()
chooser.destroy()
def run_script(self, name):
commands = open(name,'r').readlines()
for c_parse in commands:
c = c_parse.strip()
if '#' in c:
c = c[:c.find('#')].strip()
if len(c) > 0:
self.execute(cmd = c.strip())
def terminal_help(self,*args):
Help(self.terminal_help_txt)
def stop_execution(self, *args):
self.stop = True
python = execute
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