Make output precision configurable

README.md

@@ -3,44 +3,66 @@ A python utility to convert between Cartesian and Z-matrix geometries.
 
 RECENTLY ADDED: when converting from zmat to xyz, variables can now be read with no caveats.
 
-Running the below will print the output to the standard output stream (i.e. the terminal in most cases); this can be piped into a file in the usual way, e.g.
+Running the below will print the output to the standard output stream (i.e. the terminal in most cases); this can be piped into a file in the usual
+way, e.g.
 
+```bash
 python3 gc.py -xyz test.xyz > test.zmat
+```
 
 ## Usage
 
 To convert from XYZ to Z-matrix:
 
+```bash
 python3 gc.py -xyz test.xyz 
+```
 
 for files in XYZ format, i.e.
 
-Number of atoms
+```
+<Number of atoms>
 
 TITLE CARD
 
-Atom x y z
+<Atom> <x> <y> <z>
 
-Atom x y z
+<Atom> <x> <y> <z>
 
 ...
+```
 
 The default is to print the values of distances/angles/dihedrals. These can instead be printed as variables with the options
 
+```
 --rvar=True
 --avar=True
 --dvar=True
+```
 
 respectively. Alternative
 
+```
 --allvar=True
+```
 
 will set all the above to true.
 
 To convert from Z-matrix to XYZ:
 
+```bash
 python gc.py -zmat test.zmat
+```
 
-for files containing a Z-matrix. This no longer assumes that the Z-matrix has values not variables for distances/angles/dihedrals, and can read variables with no additional options. 
+for files containing a Z-matrix. This no longer assumes that the Z-matrix has values not variables for distances/angles/dihedrals, and can read
+variables with no additional options. 
 
 
+The precision of the output can be changed by means of the
+```
+--precision=12
+--angle_precision=4
+```
+options. These affect the precision of the printed out coordinates and distances and the angles respectively. The first option has effects for both
+XYZ and Z-matrix format, whereas the latter only applies to Z-matrices.
+

gc.py

@@ -36,6 +36,8 @@
 parser.add_argument("--avar", dest="avar", required=False, type=bool, default=False, help="Print angles as variables")
 parser.add_argument("--dvar", dest="dvar", required=False, type=bool, default=False, help="Print dihedrals as variables") 
 parser.add_argument("--allvar", dest="allvar", required=False, type=bool, default=False, help="Print all values as variables")
+parser.add_argument("--precision", dest="precision", required=False, type=int, default=8, help="Sets the precision of coordinates and distances")
+parser.add_argument("--angle_precision", dest="angle_precision", required=False, type=int, default=5, help="Sets the precision of angles")
 args = parser.parse_args()
 
 xyzfilename = args.xyzfile
@@ -44,14 +46,16 @@
 rvar = args.rvar or args.allvar
 avar = args.avar or args.allvar
 dvar = args.dvar or args.allvar
+precision = args.precision
+angle_precision = args.angle_precision
 
 if (xyzfilename == None and zmatfilename == None):
     print("Please specify an input geometry")
 
 elif (zmatfilename == None):
     xyzarr, atomnames = gc.readxyz(xyzfilename)
     distmat = gc.distance_matrix(xyzarr)
-    gc.write_zmat(xyzarr, distmat, atomnames, rvar=rvar, avar=avar, dvar=dvar)
+    gc.write_zmat(xyzarr, distmat, atomnames, rvar=rvar, avar=avar, dvar=dvar, distprecision=precision, angleprecision=angle_precision)
 else:
     atomnames, rconnect, rlist, aconnect, alist, dconnect, dlist = gc.readzmat(zmatfilename)
-    gc.write_xyz(atomnames, rconnect, rlist, aconnect, alist, dconnect, dlist)
+    gc.write_xyz(atomnames, rconnect, rlist, aconnect, alist, dconnect, dlist, precision=precision)

gcutil.py

@@ -158,10 +158,13 @@ def dihedral(xyzarr, i, j, k, l):
         chi = chi + 360.0
     return chi
 
-def write_zmat(xyzarr, distmat, atomnames, rvar=False, avar=False, dvar=False):
+def write_zmat(xyzarr, distmat, atomnames, rvar=False, avar=False, dvar=False, distprecision=8, angleprecision=5):
     """Prints a z-matrix from xyz coordinates, distances, and atomnames,
        optionally with the coordinate values replaced with variables.
     """
+    distformat = '{:>' + str(distprecision + 6) + '.' + str(distprecision) + 'f}'
+    angleformat = '{:>' + str(angleprecision + 6) + '.' + str(angleprecision) + 'f}'
+
     npart, ncoord = xyzarr.shape
     rlist = [] # list of bond lengths
     alist = [] # list of bond angles (degrees)
@@ -177,7 +180,7 @@ def write_zmat(xyzarr, distmat, atomnames, rvar=False, avar=False, dvar=False):
             if (rvar):
                 r = 'R1'
             else:
-                r = '{:>11.5f}'.format(rlist[0])
+                r = distformat.format(rlist[0])
             print('{:<3s} {:>4d}  {:11s}'.format(n, 1, r))
 
             if npart > 2:
@@ -187,13 +190,13 @@ def write_zmat(xyzarr, distmat, atomnames, rvar=False, avar=False, dvar=False):
                 if (rvar):
                     r = 'R2'
                 else:
-                    r = '{:>11.5f}'.format(rlist[1])
+                    r = distformat.format(rlist[1])
 
                 alist.append(angle(xyzarr, 2, 0, 1))
                 if (avar):
                     t = 'A1'
                 else:
-                    t = '{:>11.5f}'.format(alist[0])
+                    t = angleformat.format(alist[0])
 
                 print('{:<3s} {:>4d}  {:11s} {:>4d}  {:11s}'.format(n, 1, r, 2, t))
 
@@ -205,35 +208,37 @@ def write_zmat(xyzarr, distmat, atomnames, rvar=False, avar=False, dvar=False):
                         if (rvar):
                             r = 'R{:<4d}'.format(i)
                         else:
-                            r = '{:>11.5f}'.format(rlist[i-1])
+                            r = distformat.format(rlist[i-1])
 
                         alist.append(angle(xyzarr, i, i-3, i-2))
                         if (avar):
                             t = 'A{:<4d}'.format(i-1)
                         else:
-                            t = '{:>11.5f}'.format(alist[i-2])
+                            t = angleformat.format(alist[i-2])
 
                         dlist.append(dihedral(xyzarr, i, i-3, i-2, i-1))
                         if (dvar):
                             d = 'D{:<4d}'.format(i-2)
                         else:
-                            d = '{:>11.5f}'.format(dlist[i-3])
+                            d = angleformat.format(dlist[i-3])
                         print('{:3s} {:>4d}  {:11s} {:>4d}  {:11s} {:>4d}  {:11s}'.format(n, i-2, r, i-1, t, i, d))
     if (rvar):
         print(" ")
         for i in range(npart-1):
-            print('R{:<4d} = {:>11.5f}'.format(i+1, rlist[i]))
+            print('R{:<4d} = '.format(i+1) + distformat.format(rlist[i]))
     if (avar):
         print(" ")
         for i in range(npart-2):
-            print('A{:<4d} = {:>11.5f}'.format(i+1, alist[i]))
+            print('A{:<4d} = '.format(i+1) + angleformat.format(alist[i]))
     if (dvar):
         print(" ")
         for i in range(npart-3):
-            print('D{:<4d} = {:>11.5f}'.format(i+1, dlist[i]))
+            print('D{:<4d} = '.format(i+1) + angleformat.format(dlist[i]))
 
-def write_xyz(atomnames, rconnect, rlist, aconnect, alist, dconnect, dlist):
+def write_xyz(atomnames, rconnect, rlist, aconnect, alist, dconnect, dlist, precision=8):
     """Prints out an xyz file from a decomposed z-matrix"""
+    coordformat = '{:>' + str(precision + 6) + '.' + str(precision) + 'f}'
+
     npart = len(atomnames)
     print(npart)
     print('INSERT TITLE CARD HERE')
@@ -300,4 +305,4 @@ def write_xyz(atomnames, rconnect, rlist, aconnect, alist, dconnect, dlist):
 
     # print results
     for i in range(npart):
-        print('{:<4s}\t{:>11.5f}\t{:>11.5f}\t{:>11.5f}'.format(atomnames[i], xyzarr[i][0], xyzarr[i][1], xyzarr[i][2]))
+        print(('{:<4s}\t' + coordformat + '\t' + coordformat + '\t' + coordformat).format(atomnames[i], xyzarr[i][0], xyzarr[i][1], xyzarr[i][2]))