improve accuracy of sqm input coordinates (#325)

* improve accuracy of sqm input coordinates

Coordinates with 4 digits are enough for energy calculation but not enough for energy minimization.

* fix tests

* increase the string length of the number

Author: njzjz

dpdata/amber/sqm.py

@@ -94,12 +94,12 @@ def make_sqm_in(data, fname=None, frame_idx=0, **kwargs):
     ret += "     verbosity=4\n"
     ret += " /\n"
     for ii in range(len(data['atom_types'])):
-        ret += "{:>4s}{:>6s}{:>14s}{:>14s}{:>14s}\n".format(
+        ret += "{:>4s}{:>6s}{:>16s}{:>16s}{:>16s}\n".format(
             str(atomic_numbers[ii]),
             str(symbols[ii]),
-            f"{data['coords'][frame_idx][ii, 0]:.4f}",
-            f"{data['coords'][frame_idx][ii, 1]:.4f}",
-            f"{data['coords'][frame_idx][ii, 2]:.4f}"
+            f"{data['coords'][frame_idx][ii, 0]:.6f}",
+            f"{data['coords'][frame_idx][ii, 1]:.6f}",
+            f"{data['coords'][frame_idx][ii, 2]:.6f}"
         )
     if fname is not None:
         with open(fname, 'w') as fp:

tests/amber/sqm.in

@@ -5,8 +5,8 @@ Run semi-emperical minimization
      maxcyc=0
      verbosity=4
  /
-   6     C       -0.0221        0.0032        0.0165
-   1     H       -0.6690        0.8894       -0.1009
-   1     H       -0.3778       -0.8578       -0.5883
-   1     H        0.0964       -0.3151        1.0638
-   1     H        0.9725        0.2803       -0.3911
+   6     C       -0.022100        0.003200        0.016500
+   1     H       -0.669000        0.889400       -0.100900
+   1     H       -0.377800       -0.857800       -0.588300
+   1     H        0.096400       -0.315100        1.063800
+   1     H        0.972500        0.280300       -0.391100