From 224024b3efd852213d51b753fe8ed67da5ff6bb5 Mon Sep 17 00:00:00 2001
From: "T.Tian" <alchem0x2a@gmail.com>
Date: Thu, 21 Nov 2024 18:14:00 +0800
Subject: [PATCH] add example run results

---
 doc/examples/geopt_compare.md                | 24 +++++++++++++++++++-
 doc/examples/simple_dft.md                   |  9 ++++++++
 examples/simple_examples/ex1-ase-optimize.py | 21 +++++++++--------
 3 files changed, 43 insertions(+), 11 deletions(-)

diff --git a/doc/examples/geopt_compare.md b/doc/examples/geopt_compare.md
index ffb35349..8fefec60 100644
--- a/doc/examples/geopt_compare.md
+++ b/doc/examples/geopt_compare.md
@@ -14,7 +14,7 @@ from ase.build import molecule
 from ase.constraints import FixAtoms
 from sparc import SPARC
 
-nh3 = molecule("NH3", cell=(8, 8, 8), pbc=False)
+nh3 = molecule("NH3", cell=(8, 8, 8), pbc=False, center=True)
 # Fix the N center
 nh3.constraints = [FixAtoms([0])]
 nh3.rattle()
@@ -98,3 +98,25 @@ def optimize_ase_bfgs_socket():
     print(f"Final fmax: {np.max(np.abs(f_fin))} eV/Ang")
     print(f"N steps: {nsteps}")
 ```
+
+Possible outputs
+```{raw}
+SPARC internal LBFGS:
+Final energy: -330.8388527992713 eV
+Final fmax: 0.014610782237434465 eV/Ang
+N steps: 23
+```
+
+```{raw}
+ASE LBFGS
+Final energy: -330.8460713860338 eV
+Final fmax: 0.008090338967301871 eV/Ang
+N steps: 21
+```
+
+```{raw}
+ASE LBFGS (socket mode)
+Final energy: -330.8356141220578 eV
+Final fmax: 0.015431850436823448 eV/Ang
+N steps: 18
+```
diff --git a/doc/examples/simple_dft.md b/doc/examples/simple_dft.md
index d38c2ed5..9b119920 100644
--- a/doc/examples/simple_dft.md
+++ b/doc/examples/simple_dft.md
@@ -60,6 +60,15 @@ if __name__ == "__main__":
     main()
 ```
 
+The output from the above example may look like:
+```{raw}
+Fitted volume (Ang^3), energy (eV), modulus (eV/Ang^3)
+65.97840834969949 -253.07755156337953 2.9095110471623173
+Optimal cell length (cubic): 4.040799280428726 Ang
+Energy calculated by SPARC: -253.0552324051582 eV
+Energy diff 0.02231915822133601 eV
+```
+
 ```{note}
 This example uses file I/O mode for demonstration purpose only. Consider choosing the [socket mode](../advanced_socket.md) if you need more flexibility.
 ```
diff --git a/examples/simple_examples/ex1-ase-optimize.py b/examples/simple_examples/ex1-ase-optimize.py
index 750286cf..77cb06fe 100644
--- a/examples/simple_examples/ex1-ase-optimize.py
+++ b/examples/simple_examples/ex1-ase-optimize.py
@@ -7,11 +7,12 @@
 import numpy as np
 from ase.build import molecule
 from ase.constraints import FixAtoms
-from ase.optimize.bfgs import BFGS
+from ase.optimize.lbfgs import LBFGS
 
 from sparc import SPARC
 
 nh3 = molecule("NH3", cell=(8, 8, 8), pbc=False)
+nh3.center()
 # Fix the N center
 nh3.constraints = [FixAtoms([0])]
 nh3.rattle()
@@ -20,7 +21,7 @@
 def optimize_sparc_internal():
     atoms = nh3.copy()
     calc = SPARC(
-        h=0.25,
+        h=0.18,
         kpts=(1, 1, 1),
         xc="pbe",
         convergence={"forces": 0.02},
@@ -41,14 +42,14 @@ def optimize_sparc_internal():
 
 def optimize_ase_bfgs():
     atoms = nh3.copy()
-    calc = SPARC(h=0.25, kpts=(1, 1, 1), xc="pbe", directory="ex1-ase")
+    calc = SPARC(h=0.18, kpts=(1, 1, 1), xc="pbe", directory="ex1-ase")
     atoms.calc = calc
-    opt = BFGS(atoms)
+    opt = LBFGS(atoms)
     opt.run(fmax=0.02)
     e_fin = atoms.get_potential_energy()
     f_fin = atoms.get_forces()
     nsteps = opt.nsteps
-    print("ASE LBFGS")
+    print("ASE LBFGS (file I/O mode)")
     print(f"Final energy: {e_fin} eV")
     print(f"Final fmax: {np.max(np.abs(f_fin))} eV/Ang")
     print(f"N steps: {nsteps}")
@@ -57,7 +58,7 @@ def optimize_ase_bfgs():
 def optimize_ase_bfgs_socket():
     atoms = nh3.copy()
     calc = SPARC(
-        h=0.25,
+        h=0.18,
         kpts=(1, 1, 1),
         xc="pbe",
         print_forces=True,
@@ -66,18 +67,18 @@ def optimize_ase_bfgs_socket():
     )
     atoms.calc = calc
     with calc:
-        opt = BFGS(atoms)
+        opt = LBFGS(atoms)
         opt.run(fmax=0.02)
     e_fin = atoms.get_potential_energy()
     f_fin = atoms.get_forces()
     nsteps = opt.nsteps
-    print("ASE LBFGS")
+    print("ASE LBFGS (socket mode)")
     print(f"Final energy: {e_fin} eV")
     print(f"Final fmax: {np.max(np.abs(f_fin))} eV/Ang")
     print(f"N steps: {nsteps}")
 
 
 if __name__ == "__main__":
-    optimize_sparc_internal()
-    optimize_ase_bfgs()
+    # optimize_sparc_internal()
+    # optimize_ase_bfgs()
     optimize_ase_bfgs_socket()