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add more extensive whitespace checking for fortran and unittests

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This commit is contained in:
Axel Kohlmeyer
2022-10-04 04:11:39 -04:00
parent d7d2802061
commit bc6e42a610
12 changed files with 123 additions and 121 deletions
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40
python/examples/pizza/vmd.py
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@ -3,7 +3,7 @@
#
# Copyright (2005) Sandia Corporation. Under the terms of Contract
# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
# certain rights in this software. This software is distributed under
# certain rights in this software. This software is distributed under
# the GNU General Public License.
# for python3 compatibility
@ -20,24 +20,24 @@ from __future__ import print_function
oneline = "Control VMD from python"
docstr = """
v = vmd() start up VMD
v.stop() shut down VMD instance
v.clear() delete all visualizations
v = vmd() start up VMD
v.stop() shut down VMD instance
v.clear() delete all visualizations
v.rep(style) set default representation style. One of
(Lines|VDW|Licorice|DynamicBonds|Points|CPK)
v.new(file[,type]) load new file (default file type 'lammpstrj')
v.rep(style) set default representation style. One of
(Lines|VDW|Licorice|DynamicBonds|Points|CPK)
v.new(file[,type]) load new file (default file type 'lammpstrj')
v.data(file[,atomstyle]) load new data file (default atom style 'full')
v.replace(file[,type]) replace current frames with new file
v.append(file[,type]) append file to current frame(s)
v.replace(file[,type]) replace current frames with new file
v.append(file[,type]) append file to current frame(s)
v.set(snap,x,y,z,(True|False)) set coordinates from a pizza.py snapshot to new or current frame
v.frame(frame) set current frame
v.flush() flush pending input to VMD and update GUI
v.read(file) read Tcl script file (e.g. saved state)
v.enter() enter interactive shell
v.debug([True|False]) display generated VMD script commands?
v.frame(frame) set current frame
v.flush() flush pending input to VMD and update GUI
v.read(file) read Tcl script file (e.g. saved state)
v.enter() enter interactive shell
v.debug([True|False]) display generated VMD script commands?
"""
# History
@ -71,7 +71,7 @@ except ImportError:
# Class definition
class vmd:
# --------------------------------------------------------------------
def __init__(self):
@ -103,7 +103,7 @@ class vmd:
# open pipe to vmd and wait until we have a prompt
self.VMD = pexpect.spawn(self.vmdexe)
self.VMD.expect('vmd >')
# --------------------------------------------------------------------
# post command to vmd and wait until the prompt returns.
def __call__(self,command):
@ -113,7 +113,7 @@ class vmd:
if self.debugme:
print("call+result:"+self.VMD.before)
return
# --------------------------------------------------------------------
# exit VMD
def stop(self):
@ -198,7 +198,7 @@ class vmd:
self.__call__('mol addfile ' + filename + ' mol $tmol type ' + filetype + ' waitfor all')
self.__call__('foreach mol [molinfo list] { molinfo $mol set {center_matrix rotate_matrix scale_matrix global_matrix} $viewpoints($mol)}')
self.flush()
# --------------------------------------------------------------------
# replace all frames of a molecule with those from a given file
def update(self,filename,filetype='lammpstrj'):
@ -209,7 +209,7 @@ class vmd:
self.__call__('mol addfile ' + filename + ' mol $tmol type ' + filetype + ' waitfor all')
self.__call__('foreach mol [molinfo list] {molinfo $mol set {center_matrix rotate_matrix scale_matrix global_matrix} $viewpoints($mol)}')
self.flush()
# --------------------------------------------------------------------
# add or overwrite coordinates with coordinates in a snapshot
def set(self,snap,x,y,z,append=True):