From bc6e42a6104999f5d35ca9a9997a275e7ca9854d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 4 Oct 2022 04:11:39 -0400 Subject: [PATCH] add more extensive whitespace checking for fortran and unittests --- python/examples/mc.py | 4 +- python/examples/pizza/gl.py | 144 +++++++++--------- python/examples/pizza/vizinfo.py | 28 ++-- python/examples/pizza/vmd.py | 40 ++--- python/examples/pylammps/elastic/README | 2 +- python/examples/split.py | 6 +- python/examples/viz_gl.py | 2 +- python/examples/viz_pymol.py | 4 +- tools/coding_standard/whitespace.py | 4 +- .../fortran/test_fortran_extract_variable.f90 | 4 +- unittest/tools/test_lammps_shell.py | 2 +- unittest/utils/testshared.c | 4 +- 12 files changed, 123 insertions(+), 121 deletions(-) diff --git a/python/examples/mc.py b/python/examples/mc.py index fe7f6838c8..c12b4bd6bc 100755 --- a/python/examples/mc.py +++ b/python/examples/mc.py @@ -60,7 +60,7 @@ lmp.command("thermo_style custom step v_emin v_elast pe") lmp.command("run 0") x = lmp.extract_atom("x") lmp.command("variable elast equal $e") - + estart = lmp.extract_compute("thermo_pe", LMP_STYLE_GLOBAL, LAMMPS_INT) / natoms # loop over Monte Carlo moves @@ -92,7 +92,7 @@ for i in range(nloop): else: x[iatom][0] = x0 x[iatom][1] = y0 - + # final energy and stats lmp.command("variable nbuild equal nbuild") diff --git a/python/examples/pizza/gl.py b/python/examples/pizza/gl.py index 7c5633ac55..c567c0805f 100644 --- a/python/examples/pizza/gl.py +++ b/python/examples/pizza/gl.py @@ -3,7 +3,7 @@ # # Copyright (2005) Sandia Corporation. Under the terms of Contract # DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains -# certain rights in this software. This software is distributed under +# certain rights in this software. This software is distributed under # the GNU General Public License. # for python3 compatibility @@ -19,8 +19,8 @@ g = gl(d) create OpenGL display for data in d d = atom snapshot object (dump, data) g.bg("black") set background color (def = "black") -g.size(N) set image size to NxN -g.size(N,M) set image size to NxM +g.size(N) set image size to NxN +g.size(N,M) set image size to NxM g.rotate(60,135) view from z theta and azimuthal phi (def = 60,30) g.shift(x,y) translate by x,y pixels in view window (def = 0,0) g.zoom(0.5) scale image by factor (def = 1) @@ -30,7 +30,7 @@ g.box(0/1/2,"red",4) set box edge thickness g.file = "image" file prefix for created images (def = "image") g.show(N) show image of snapshot at timestep N - + g.all() make images of all selected snapshots g.all(P) images of all, start file label at P g.all(N,M,P) make M images of snapshot N, start label at P @@ -43,12 +43,12 @@ g.pan() no pan during all() (default) g.select = "$x > %g*3.0" string to pass to d.aselect.test() during all() g.select = "" no extra aselect (default) - + %g varies from 0.0 to 1.0 from beginning to end of all() - -g.acol(2,"green") set atom colors by atom type (1-N) -g.acol([2,4],["red","blue"]) 1st arg = one type or list of types -g.acol(0,"blue") 2nd arg = one color or list of colors + +g.acol(2,"green") set atom colors by atom type (1-N) +g.acol([2,4],["red","blue"]) 1st arg = one type or list of types +g.acol(0,"blue") 2nd arg = one color or list of colors g.acol(range(20),["red","blue"]) if list lengths unequal, interpolate g.acol(range(10),"loop") assign colors in loop, randomly ordered @@ -58,23 +58,23 @@ g.acol(range(10),"loop") assign colors in loop, randomly ordered g.arad([1,2],[0.5,0.3]) set atom radii, same rules as acol() -g.bcol() set bond color, same args as acol() -g.brad() set bond thickness, same args as arad() +g.bcol() set bond color, same args as acol() +g.brad() set bond thickness, same args as arad() -g.tcol() set triangle color, same args as acol() -g.tfill() set triangle fill, 0 fill, 1 line, 2 both +g.tcol() set triangle color, same args as acol() +g.tfill() set triangle fill, 0 fill, 1 line, 2 both g.lcol() set line color, same args as acol() g.lrad() set line thickness, same args as arad() g.adef() set atom/bond/tri/line properties to default -g.bdef() default = "loop" for colors, 0.45 for radii -g.tdef() default = 0.25 for bond/line thickness -g.ldef() default = 0 fill +g.bdef() default = "loop" for colors, 0.45 for radii +g.tdef() default = 0.25 for bond/line thickness +g.ldef() default = 0 fill by default 100 types are assigned if atom/bond/tri/line has type > # defined properties, is an error - + from vizinfo import colors access color list print(colors) list defined color names and RGB values colors["nickname"] = [R,G,B] set new RGB values from 0 to 255 @@ -148,7 +148,7 @@ class gl: self.azphi = 30 self.scale = 1.0 self.xshift = self.yshift = 0 - + self.file = "image" self.boxflag = 0 self.bxcol = [1,1,0] @@ -165,7 +165,7 @@ class gl: self.nsides = 10 self.theta_amplify = 2 self.shiny = 2 - + self.clipflag = 0 self.clipxlo = self.clipylo = self.clipzlo = 0.0 self.clipxhi = self.clipyhi = self.clipzhi = 1.0 @@ -189,7 +189,7 @@ class gl: self.bdef() self.tdef() self.ldef() - + self.center = 3*[0] self.view = 3*[0] self.up = 3*[0] @@ -211,7 +211,7 @@ class gl: if not ynew: self.ypixels = self.xpixels else: self.ypixels = ynew self.create_window() - + # -------------------------------------------------------------------- def axis(self,value): @@ -223,7 +223,7 @@ class gl: def create_window(self): if self.root: self.root.destroy() - + from __main__ import tkroot self.root = Toplevel(tkroot) self.root.title('Pizza.py gl tool') @@ -232,7 +232,7 @@ class gl: double=1,depth=1) self.w.pack(expand=YES) # self.w.pack(expand=YES,fill=BOTH) - + glViewport(0,0,self.xpixels,self.ypixels) glEnable(GL_LIGHTING); glEnable(GL_LIGHT0); @@ -247,7 +247,7 @@ class gl: self.w.parent = self self.w.tkRedraw() tkroot.update_idletasks() # force window to appear - + # -------------------------------------------------------------------- def clip(self,which,value): @@ -314,7 +314,7 @@ class gl: self.up[1] = sin(pi*self.azphi/180) self.up[2] = 0.0 else: - dot = self.view[2] # dot = (0,0,1) . view + dot = self.view[2] # dot = (0,0,1) . view self.up[0] = -dot*self.view[0] # up projected onto v = dot * v self.up[1] = -dot*self.view[1] # up perp to v = up - dot * v self.up[2] = 1.0 - dot*self.view[2] @@ -325,7 +325,7 @@ class gl: # -------------------------------------------------------------------- # reset ztheta,azphi and thus view,up.right # called as function from Pizza.py - + def rotate(self,ztheta,azphi): self.ztheta = ztheta self.azphi = azphi @@ -366,11 +366,11 @@ class gl: # rotate view,up around axis of rotation = old x new # right = up x view # reset ztheta,azphi from view - + def mouse_rotate(self,xnew,ynew,xold,yold): # change y pixels to measure from bottom of window instead of top - + yold = self.ypixels - yold ynew = self.ypixels - ynew @@ -407,7 +407,7 @@ class gl: axis[1] = rot[0]*self.right[1] + rot[1]*self.up[1] + rot[2]*self.view[1] axis[2] = rot[0]*self.right[2] + rot[1]*self.up[2] + rot[2]*self.view[2] axis = vecnorm(axis) - + # view is changed by (axis x view) scaled by theta # up is changed by (axis x up) scaled by theta # force up to be perp to view via up_perp = up - (up . view) view @@ -468,14 +468,14 @@ class gl: # output: eye = distance to view scene from # xto,yto,zto = point to look to # xfrom,yfrom,zfrom = point to look from - + def setview(self): if not self.ready: return # no distance since no scene yet - + self.eye = 3 * self.distance / self.scale xfactor = 0.5*self.eye*self.xshift/self.xpixels yfactor = 0.5*self.eye*self.yshift/self.ypixels - + self.xto = self.center[0] - xfactor*self.right[0] - yfactor*self.up[0] self.yto = self.center[1] - xfactor*self.right[1] - yfactor*self.up[1] self.zto = self.center[2] - xfactor*self.right[2] - yfactor*self.up[2] @@ -486,7 +486,7 @@ class gl: # -------------------------------------------------------------------- # box attributes, also used for triangle lines - + def box(self,*args): self.boxflag = args[0] if len(args) > 1: @@ -500,7 +500,7 @@ class gl: # -------------------------------------------------------------------- # grab all selected snapshots from data object # add GL-specific info to each bond - + def reload(self): print("Loading data into gl tool ...") data = self.data @@ -529,7 +529,7 @@ class gl: self.bondframes.append(bonds) self.triframes.append(tris) self.lineframes.append(lines) - + print(time,end='') sys.stdout.flush() print() @@ -545,11 +545,11 @@ class gl: def nolabel(self): self.cachelist = -self.cachelist self.labels = [] - + # -------------------------------------------------------------------- # show a single snapshot # distance from snapshot box or max box for all selected steps - + def show(self,ntime): data = self.data which = data.findtime(ntime) @@ -571,7 +571,7 @@ class gl: self.cachelist = -self.cachelist self.w.tkRedraw() self.save() - + # -------------------------------------------------------------------- def pan(self,*list): @@ -584,7 +584,7 @@ class gl: self.ztheta_stop = list[3] self.azphi_stop = list[4] self.scale_stop = list[5] - + # -------------------------------------------------------------------- def all(self,*list): @@ -615,7 +615,7 @@ class gl: if flag == -1: break fraction = float(i) / (ncount-1) - + if self.select != "": newstr = self.select % fraction data.aselect.test(newstr,time) @@ -653,7 +653,7 @@ class gl: self.cachelist = -self.cachelist self.w.tkRedraw() self.save(file) - + print(time,end='') sys.stdout.flush() i += 1 @@ -731,19 +731,19 @@ class gl: # -------------------------------------------------------------------- # draw the GL scene - + def redraw(self,o): # clear window to background color - + glClearColor(self.bgcol[0],self.bgcol[1],self.bgcol[2],0) glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT) # not ready if no scene yet - + if not self.ready: return # set view from eye, distance, 3 lookat vectors (from,to,up) - + glMatrixMode(GL_PROJECTION) glLoadIdentity() if self.orthoflag: @@ -759,14 +759,14 @@ class gl: # draw scene from display list if caching allowed and list hasn't changed # else redraw and store as new display list if caching allowed - + if self.cache and self.cachelist > 0: glCallList(self.cachelist); else: if self.cache: if self.cachelist < 0: glDeleteLists(-self.cachelist,1) self.cachelist = glGenLists(1) glNewList(self.cachelist,GL_COMPILE_AND_EXECUTE) - + # draw box, clip-box, xyz axes, lines glDisable(GL_LIGHTING) @@ -842,7 +842,7 @@ class gl: if self.tridraw: fillflag = self.vizinfo.tfill[int(self.tridraw[0][1])] - + if fillflag != 1: if fillflag: glEnable(GL_POLYGON_OFFSET_FILL) @@ -921,7 +921,7 @@ class gl: gluCylinder(obj,rad,rad,bond[10],self.nsides,self.nsides) glPopMatrix() - if self.tridraw: + if self.tridraw: fillflag = self.vizinfo.tfill[int(self.tridraw[0][1])] if fillflag != 1: @@ -975,7 +975,7 @@ class gl: glEnd() glEnable(GL_LIGHTING) glPolygonMode(GL_FRONT_AND_BACK,GL_FILL) - + if self.cache: glEndList() glFlush() @@ -983,16 +983,16 @@ class gl: # -------------------------------------------------------------------- # make new call list for each atom type # called when atom color/rad/quality is changed - + def make_atom_calllist(self): # extend calllist array if necessary - + if self.vizinfo.nacolor > self.nclist: for i in range(self.vizinfo.nacolor-self.nclist): self.calllist.append(0) self.nclist = self.vizinfo.nacolor # create new calllist for each atom type - + for itype in xrange(1,self.vizinfo.nacolor+1): if self.calllist[itype]: glDeleteLists(self.calllist[itype],1) ilist = glGenLists(1) @@ -1001,12 +1001,12 @@ class gl: red,green,blue = self.vizinfo.acolor[itype] rad = self.vizinfo.arad[itype] glColor3f(red,green,blue); - + # glPointSize(10.0*rad) # glBegin(GL_POINTS) # glVertex3f(0.0,0.0,0.0) # glEnd() - + glMaterialfv(GL_FRONT,GL_EMISSION,[red,green,blue,1.0]); glMaterialf(GL_FRONT,GL_SHININESS,self.shiny); glutSolidSphere(rad,self.nslices,self.nstacks) @@ -1015,7 +1015,7 @@ class gl: # -------------------------------------------------------------------- # augment bond info returned by viz() with info needed for GL draw # info = length, theta, -dy, dx for bond orientation - + def bonds_augment(self,bonds): for bond in bonds: dx = bond[5] - bond[2] @@ -1046,7 +1046,7 @@ class gl: glLineWidth(self.bxthick) glColor3f(self.bxcol[0],self.bxcol[1],self.bxcol[2]) - + glBegin(GL_LINE_LOOP) glVertex3f(xlo,ylo,zlo) glVertex3f(xhi,ylo,zlo) @@ -1081,7 +1081,7 @@ class gl: if yhi-ylo > delta: delta = yhi-ylo if zhi-zlo > delta: delta = zhi-zlo delta *= 0.1 - + glLineWidth(self.bxthick) glBegin(GL_LINES) @@ -1100,7 +1100,7 @@ class gl: def save(self,file=None): self.w.update() # force image on screen to be current before saving it - + pstring = glReadPixels(0,0,self.xpixels,self.ypixels, GL_RGBA,GL_UNSIGNED_BYTE) snapshot = Image.fromstring("RGBA",(self.xpixels,self.ypixels),pstring) @@ -1110,14 +1110,14 @@ class gl: snapshot.save(file + ".png") # -------------------------------------------------------------------- - + def adef(self): self.vizinfo.setcolors("atom",range(100),"loop") self.vizinfo.setradii("atom",range(100),0.45) self.make_atom_calllist() self.cachelist = -self.cachelist self.w.tkRedraw() - + # -------------------------------------------------------------------- def bdef(self): @@ -1130,14 +1130,14 @@ class gl: def tdef(self): self.vizinfo.setcolors("tri",range(100),"loop") - self.vizinfo.setfills("tri",range(100),0) + self.vizinfo.setfills("tri",range(100),0) self.cachelist = -self.cachelist self.w.tkRedraw() # -------------------------------------------------------------------- def ldef(self): - self.vizinfo.setcolors("line",range(100),"loop") + self.vizinfo.setcolors("line",range(100),"loop") self.vizinfo.setradii("line",range(100),0.25) self.cachelist = -self.cachelist self.w.tkRedraw() @@ -1149,29 +1149,29 @@ class gl: self.make_atom_calllist() self.cachelist = -self.cachelist self.w.tkRedraw() - + # -------------------------------------------------------------------- def arad(self,atypes,radii): - self.vizinfo.setradii("atom",atypes,radii) + self.vizinfo.setradii("atom",atypes,radii) self.make_atom_calllist() self.cachelist = -self.cachelist self.w.tkRedraw() - + # -------------------------------------------------------------------- def bcol(self,btypes,colors): self.vizinfo.setcolors("bond",btypes,colors) self.cachelist = -self.cachelist self.w.tkRedraw() - + # -------------------------------------------------------------------- def brad(self,btypes,radii): self.vizinfo.setradii("bond",btypes,radii) self.cachelist = -self.cachelist self.w.tkRedraw() - + # -------------------------------------------------------------------- def tcol(self,ttypes,colors): @@ -1210,10 +1210,10 @@ class MyOpengl(Opengl): args = (self,master,cnf) Opengl.__init__(*args,**kw) Opengl.autospin_allowed = 0 - + # redraw Opengl scene # call parent redraw() method - + def tkRedraw(self,*dummy): if not self.initialised: return self.tk.call(self._w,'makecurrent') @@ -1222,7 +1222,7 @@ class MyOpengl(Opengl): # left button translate # access parent xshift/yshift and call parent trans() method - + def tkTranslate(self,event): dx = event.x - self.xmouse dy = event.y - self.ymouse @@ -1242,7 +1242,7 @@ class MyOpengl(Opengl): # right button zoom # access parent scale and call parent zoom() method - + def tkScale(self,event): scale = 1 - 0.01 * (event.y - self.ymouse) if scale < 0.001: scale = 0.001 diff --git a/python/examples/pizza/vizinfo.py b/python/examples/pizza/vizinfo.py index a150a9c84f..e3a05d71ce 100644 --- a/python/examples/pizza/vizinfo.py +++ b/python/examples/pizza/vizinfo.py @@ -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. # vizinfo class, not a top-level Pizza.py tool @@ -25,7 +25,7 @@ import types class vizinfo: """ Information holder for Pizza.py visualization tools - + acolor,bcolor,tcolor,lcolor = RGB values for each atom/bond/tri/line type arad = radius of each atom type brad,lrad = thickness of each bond/line type @@ -41,7 +41,7 @@ class vizinfo: setfill() = set triangle fill factor extend() = grow an array """ - + # -------------------------------------------------------------------- def __init__(self): @@ -57,15 +57,15 @@ class vizinfo: self.nbcolor = self.nbrad = 0 self.ntcolor = self.ntfill = 0 self.nlcolor = self.nlrad = 0 - + # -------------------------------------------------------------------- # set color RGB for which = atoms, bonds, triangles - + def setcolors(self,which,ids,rgbs): # convert args into lists if single values # if arg = 0, convert to full-range list - + if type(ids) is types.IntType and ids == 0: if which == "atom": ids = range(self.nacolor) if which == "bond": ids = range(self.nbcolor) @@ -101,11 +101,11 @@ class vizinfo: if max(ids) > self.nlcolor: self.nlcolor = self.extend(self.lcolor,max(ids)) self.nlcolor = self.extend(self.lrad,max(ids)) - + # set color for each type # if list lengths match, set directly, else interpolate # convert final color from 0-255 to 0.0-1.0 - + ntypes = len(ids) nrgbs = len(rgbs) @@ -135,7 +135,7 @@ class vizinfo: if which == "bond": self.bcolor[id] = color if which == "tri": self.tcolor[id] = color if which == "line": self.lcolor[id] = color - + # -------------------------------------------------------------------- # set radii for which = atoms, bonds, lines @@ -143,7 +143,7 @@ class vizinfo: # convert args into lists if single values # if arg = 0, convert to full-range list - + if type(ids) is types.IntType and ids == 0: if which == "atom": ids = range(self.narad) if which == "bond": ids = range(self.nbrad) @@ -199,16 +199,16 @@ class vizinfo: if which == "atom": self.arad[id] = rad if which == "bond": self.brad[id] = rad if which == "line": self.lrad[id] = rad - + # -------------------------------------------------------------------- # set triangle fill style # 0 = fill only, 1 = line only, 2 = fill and line - + def setfills(self,which,ids,fills): # convert args into lists if single values # if arg = 0, convert to full-range list - + if type(ids) is types.IntType and ids == 0: ids = range(self.ntfill) if type(ids) is not types.ListType and type(ids) is not types.TupleType: @@ -237,7 +237,7 @@ class vizinfo: for i in range(len(ids)): self.tfill[ids[i]] = int(fills[i]) else: for id in ids: self.tfill[id] = int(fills[0]) - + # -------------------------------------------------------------------- def extend(self,array,n): diff --git a/python/examples/pizza/vmd.py b/python/examples/pizza/vmd.py index 00b8615092..5c8461f6ca 100644 --- a/python/examples/pizza/vmd.py +++ b/python/examples/pizza/vmd.py @@ -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): diff --git a/python/examples/pylammps/elastic/README b/python/examples/pylammps/elastic/README index 8d1712cd10..40ba34fa62 100644 --- a/python/examples/pylammps/elastic/README +++ b/python/examples/pylammps/elastic/README @@ -1,4 +1,4 @@ conversion of lammps scripts to python code using PyLammps interface -Example for elastic.py +Example for elastic.py python elastic.py Au.data EAM_Dynamo_Ackland_1987_Au__MO_754413982908_000 Au diff --git a/python/examples/split.py b/python/examples/split.py index bd2896c004..2e63d57621 100755 --- a/python/examples/split.py +++ b/python/examples/split.py @@ -32,7 +32,7 @@ nprocs = comm.Get_size() if me < nprocs // 2: color = 0 else: color = 1 - + split = comm.Split(color,key=0) if color == 0: @@ -69,12 +69,12 @@ else: # could run a 2nd calculation on second partition # with different LAMMPS instance or another code # in this case, just sleep on second partition - + import time time.sleep(2) print("Calculation on partition 1 complete") # shutdown mpi4py - + comm.Barrier() MPI.Finalize() diff --git a/python/examples/viz_gl.py b/python/examples/viz_gl.py index 6266682b9c..ab527e0329 100755 --- a/python/examples/viz_gl.py +++ b/python/examples/viz_gl.py @@ -50,7 +50,7 @@ ntimestep = 0 if me == 0: tkroot = None - try: + try: import Tkinter except: import tkinter as Tkinter diff --git a/python/examples/viz_pymol.py b/python/examples/viz_pymol.py index b5061d4c20..1b139dc37e 100755 --- a/python/examples/viz_pymol.py +++ b/python/examples/viz_pymol.py @@ -63,7 +63,7 @@ if me == 0: p.single(ntimestep) pm.load("tmp.pdb") pm.show("spheres","tmp") - + # run nfreq steps at a time w/out pre/post, read dump snapshot, display it while ntimestep < nsteps: @@ -75,7 +75,7 @@ while ntimestep < nsteps: p.single(ntimestep) pm.load("tmp.pdb") pm.forward() - + lmp.command("run 0 pre no post yes") # uncomment if running in parallel via mpi4py diff --git a/tools/coding_standard/whitespace.py b/tools/coding_standard/whitespace.py index be53f60380..1c980717d6 100644 --- a/tools/coding_standard/whitespace.py +++ b/tools/coding_standard/whitespace.py @@ -24,11 +24,13 @@ include: - cmake/** - doc - doc/src/** - - python + - fortran/** + - python/** - src/** - lib/** - tools/coding_standard - tools/python + - unittest/** exclude: - lib/colvars/Install.py - lib/gpu/geryon/file_to_cstr.sh diff --git a/unittest/fortran/test_fortran_extract_variable.f90 b/unittest/fortran/test_fortran_extract_variable.f90 index 34ccb766de..ded3743409 100644 --- a/unittest/fortran/test_fortran_extract_variable.f90 +++ b/unittest/fortran/test_fortran_extract_variable.f90 @@ -100,7 +100,7 @@ FUNCTION f_lammps_with_C_args(argc, argv) BIND(C) TYPE(c_ptr), INTENT(IN), VALUE :: str INTEGER(c_size_t) :: c_strlen END FUNCTION c_strlen - END INTERFACE + END INTERFACE CALL C_F_POINTER(argv, Fargv, [argc]) DO i = 1, argc @@ -111,7 +111,7 @@ FUNCTION f_lammps_with_C_args(argc, argv) BIND(C) args(i)(j:j) = Cstr(j) END FORALL END DO - + lmp = lammps(args) f_lammps_with_C_args = lmp%handle END FUNCTION f_lammps_with_C_args diff --git a/unittest/tools/test_lammps_shell.py b/unittest/tools/test_lammps_shell.py index 15cb259f84..2a55be0a4e 100644 --- a/unittest/tools/test_lammps_shell.py +++ b/unittest/tools/test_lammps_shell.py @@ -138,7 +138,7 @@ class LammpsShell(unittest.TestCase): for line in lines: if line.startswith('LAMMPS Shell>'): break idx += 1 - + self.assertEqual(lines[idx+4],"dimension 2") self.assertEqual(lines[idx+6],"units real") self.assertEqual(lines[idx+8],"dimension 2") diff --git a/unittest/utils/testshared.c b/unittest/utils/testshared.c index 869be91c2a..12922dea91 100644 --- a/unittest/utils/testshared.c +++ b/unittest/utils/testshared.c @@ -16,5 +16,5 @@ double some_double_function(double arg1, int arg2) return sum; } - - + +