update examples with preopt option

Author: qzhu2017

examples/0-aspirin-simple.py

@@ -2,10 +2,9 @@
 This is an example to perform CSP based on the reference crystal.
 The structures with good matches will be output to *-matched.cif.
 """
-import warnings
-warnings.filterwarnings("ignore", category=UserWarning, module='torchani.aev')
 from pyxtal.optimize import WFS, DFS, QRS
 from pyxtal.representation import representation
+from pyxtal.molecule import pyxtal_molecule
 import argparse
 import os
 
@@ -19,16 +18,17 @@
                       help="cpu number, default: 1")
     parser.add_argument("-a", "--algo", dest="algo", default='WFS',
                       help="algorithm, default: WFS")
+    parser.add_argument("--preopt", dest='preopt', action='store_true',
+                      help="preoptimize the lattice and rotation")
+
     options = parser.parse_args()
     smiles, sg, wdir = "CC(=O)OC1=CC=CC=C1C(=O)O", [14], "aspirin-simple"
     # Reconstruct the reference structure
     x = "81 11.38  6.48 11.24  96.9 1 0 0.23 0.43 0.03  -44.6   25.0   34.4  -76.6   -5.2  171.5 0"
     rep = representation.from_string(x, [smiles])
     xtal = rep.to_pyxtal()
     pmg = xtal.to_pymatgen()
-
-    # Check if use_mpi is invoked
-    use_mpi = "OMPI_COMM_WORLD_SIZE" in os.environ or "SLURM_MPI_TYPE" in os.environ
+    m1 = pyxtal_molecule('CC(=O)OC1=CC=CC=C1C(=O)O.smi', active_sites=[[11], [12], [20]])
 
     # Sampling
     fun = globals().get(options.algo)
@@ -40,7 +40,8 @@
              N_pop = options.pop,
              N_cpu = options.ncpu,
              ff_style = 'gaff',
-             use_mpi = use_mpi)
+             molecules = [[m1]] if options.preopt else None,
+             pre_opt = options.preopt)
 
     go.run(ref_pmg=pmg)
     go.print_matches(header='Ref_match')

examples/4-preopt-xxv.py

@@ -0,0 +1,35 @@
+from pyxtal.optimize import DFS, WFS
+from pyxtal.db import database
+from time import time
+from pyxtal.molecule import pyxtal_molecule
+import warnings
+warnings.filterwarnings("ignore", category=UserWarning, module='torchani.aev')
+if __name__ == "__main__":
+    code = 'XAFQAZ'
+    db = database('data/benchmark.db')
+    pmg = db.get_pyxtal(code).to_pymatgen()
+    row = db.get_row(code)
+    m1 = pyxtal_molecule('OC(=O)c1cc(cc(c1)N(=O)=O)N(=O)=O.smi', active_sites=[[], [0], [15]])
+    m2 = pyxtal_molecule('Cc1ccc2N3CN(Cc2c1)c1ccc(C)cc1C3.smi', active_sites=[[5], [], []])
+    go = DFS(m1.smile + '.' + m2.smile,
+         code+'-00',
+         [14],
+         code,
+         N_gen = 5,
+         N_pop = 256,
+         N_cpu = 128,
+         ff_style = 'gaff',
+         molecules = [[m1], [m2]],
+         pre_opt = True,
+         )
+    t0 = time()
+    suc_rate = go.run(ref_pmg=pmg)
+    if len(go.matches) > 0:
+        best_rank = go.print_matches()
+        mytag = f"Succ_rate: {suc_rate:7.4f}% True {best_rank:d}/{go.N_struc:d}"
+    else:
+        mytag = f"False 0/{go.N_struc:d}"
+    eng = go.min_energy
+    t1 = int((time() - t0)/60)
+    strs = "Final {:8s} {:12.3f} {:20s}".format(code, eng, mytag)
+    print(strs)

examples/README.md

@@ -59,6 +59,13 @@ python 3-benchmark.py -g 20 -p 192 -n 192 -a WFS -c FLUANT
 ```
 This will just run one system called `FLUANT` with 20 generations.
 
+### `4-preopt-xxv.py`
+This is an example to explore the use of pre_opt option that can preoptimize the randomly built crystal based on `optimize_lattice_rotation` function.
+
+```
+python 4-preopt-xxv.py > log-4-xxv
+```
+
 
 ## How to run it on the HPC nodes??
 

tests/README.md

@@ -1,6 +1,4 @@
-# Test Charmm Installation
-
-This is a directory to test the installation of CHARMM
+## Test Charmm Installation
 
 1. add charmm executable to your system PATH.
 ```
@@ -22,3 +20,19 @@ $ charmm < charmm.in
 
 You should see quickly see the output of `NORMAL TERMINATION`. 
 If you see other kinds of output, please go back to reinstall charmm.
+
+
+## Test the use of `optimize_lattice_and_rotation()`
+In PyXtal_v1.0.5 or higher, we have implemented the optimize_lattice_and_rotation() to allow the optimization of random crystal by
+1. cut the empty spacing of the crystal lattice
+2. optimize the molecular orientation to encourage the formation of strong H-bond (with the specified Hbond acceptor, hydrogen and donor sites)
+
+After applying this function, one should expect to get a more reasonable structure that can be used for the subsequent CSP calculation. This may be useful to reduce the searching space.
+
+To test if this function is working, run the following commond in this folder.
+```
+$ python test_opt_lattice_rotation.py 
+```
+
+
+

tests/test_opt_lattice_rotation.py

@@ -0,0 +1,24 @@
+"""
+A quick example to test if the optimize_lattice_and_rotation works in PyXtal
+"""
+
+from pyxtal import pyxtal
+from pyxtal.molecule import pyxtal_molecule
+
+xtal = pyxtal(molecular=True)
+
+# apsirin
+asp = pyxtal_molecule('CC(=O)OC1=CC=CC=C1C(=O)O.smi', active_sites=[[11], [12], [20]])
+#xtal.from_random(3, 14, [asp], sites=[["4e"]])
+xtal.from_random(3, 14, [asp], [8], sites=[["4e", "4e"]])
+xtal.to_file('init_asp.cif'); print("Init: ", xtal.lattice, xtal.get_orientation_energy())
+xtal.optimize_lattice_and_rotation()
+xtal.to_file('opt_asp.cif');  print("Opt:  ", xtal.lattice, xtal.get_orientation_energy())
+
+# XXV
+m1 = pyxtal_molecule('OC(=O)c1cc(cc(c1)N(=O)=O)N(=O)=O.smi', active_sites=[[], [0], [15]])
+m2 = pyxtal_molecule('Cc1ccc2N3CN(Cc2c1)c1ccc(C)cc1C3.smi', active_sites=[[5], [], []])
+xtal.from_random(3, 14, [m1, m2], [4, 4], sites=[["4e"], ["4e"]])
+xtal.to_file('init_xxv.cif'); print("Init: ", xtal.lattice, xtal.get_orientation_energy())
+xtal.optimize_lattice_and_rotation()
+xtal.to_file('opt_xxv.cif');  print("Opt:  ", xtal.lattice, xtal.get_orientation_energy())