add examples inside geop

litman90 · Nov 12, 2024 · 783fc69 · 783fc69
1 parent 9c91377
commit 783fc69
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Showing 8 changed files with 107 additions and 2 deletions.
diff --git a/examples/features/geometry_optimization/SD_pswater_with_fixatoms/init.xyz b/examples/features/geometry_optimization/SD_pswater_with_fixatoms/init.xyz
@@ -0,0 +1,5 @@
+3
+# CELL(abcABC):   35.23300    35.23300    35.23300    90.00000    90.00000    90.00000  Traj: positions{angstrom} Step:          11  Bead:       0 
+       O  0.00000e+00 -2.00000e-02  0.00000e+00
+       H  7.50000e-01  5.00000e-01  0.00000e+00
+       H -7.50000e-01  5.00000e-01  0.00000e+00
diff --git a/examples/features/geometry_optimization/SD_pswater_with_fixatoms/input.xml b/examples/features/geometry_optimization/SD_pswater_with_fixatoms/input.xml
@@ -0,0 +1,31 @@
+<simulation mode='static' verbosity='high'>
+  <output prefix='simulation'>
+    <properties stride='1' filename='out'>  [ step, potential ] </properties>
+    <trajectory filename='pos' stride='1'> positions </trajectory>
+  </output>
+  <total_steps> 1000 </total_steps>
+  <prng>
+    <seed> 32342 </seed>
+  </prng>
+  <ffsocket name='pswater' mode='unix' pbc='false'>
+    <address> h2o-geop </address>
+  </ffsocket>
+  <system>
+    <initialize nbeads='1'>
+      <file mode='xyz'> init.xyz </file>
+    </initialize>
+    <forces>
+      <force forcefield='pswater'> </force>
+    </forces>
+    <motion mode='minimize'>
+       <fixatoms>[0]</fixatoms>
+      <optimizer mode='sd'>
+        <tolerances>
+          <energy> 1e-5 </energy>
+          <force> 1e-5 </force>
+          <position> 1e-5 </position>
+        </tolerances>
+      </optimizer>
+    </motion>
+  </system>
+</simulation>
diff --git a/examples/features/geometry_optimization/SD_pswater_with_fixatoms/run.sh b/examples/features/geometry_optimization/SD_pswater_with_fixatoms/run.sh
@@ -0,0 +1,16 @@
+ipi=i-pi
+driver="i-pi-driver -m pswater -u -a h2o-geop"
+sleep_time=4
+
+${ipi} input.xml > log.i-pi & 
+echo "# i-PI is running"
+
+echo "# Waiting for ${sleep_time} (s) before executing driver"
+sleep ${sleep_time}
+
+${driver} > /dev/null & 
+echo "# Driver is running"
+
+wait
+
+echo "# Simulation complete"
diff --git a/examples/features/geometry_optimization/SD_pswater_with_fixdofs/init.xyz b/examples/features/geometry_optimization/SD_pswater_with_fixdofs/init.xyz
@@ -0,0 +1,5 @@
+3
+# CELL(abcABC):   35.23300    35.23300    35.23300    90.00000    90.00000    90.00000  Traj: positions{angstrom} Step:          11  Bead:       0 
+       O  0.00000e+00 -2.00000e-02  0.00000e+00
+       H  7.50000e-01  5.00000e-01  0.00000e+00
+       H -7.50000e-01  5.00000e-01  0.00000e+00
diff --git a/examples/features/geometry_optimization/SD_pswater_with_fixdofs/input.xml b/examples/features/geometry_optimization/SD_pswater_with_fixdofs/input.xml
@@ -0,0 +1,31 @@
+<simulation mode='static' verbosity='high'>
+  <output prefix='simulation'>
+    <properties stride='1' filename='out'>  [ step, potential ] </properties>
+    <trajectory filename='pos' stride='1'> positions </trajectory>
+  </output>
+  <total_steps> 1000 </total_steps>
+  <prng>
+    <seed> 32342 </seed>
+  </prng>
+  <ffsocket name='pswater' mode='unix' pbc='false'>
+    <address> h2o-geop </address>
+  </ffsocket>
+  <system>
+    <initialize nbeads='1'>
+      <file mode='xyz'> init.xyz </file>
+    </initialize>
+    <forces>
+      <force forcefield='pswater'> </force>
+    </forces>
+    <motion mode='minimize'>
+       <fixatoms_dof>[0,1,2]</fixatoms_dof>
+      <optimizer mode='sd'>
+        <tolerances>
+          <energy> 1e-5 </energy>
+          <force> 1e-5 </force>
+          <position> 1e-5 </position>
+        </tolerances>
+      </optimizer>
+    </motion>
+  </system>
+</simulation>
diff --git a/examples/features/geometry_optimization/SD_pswater_with_fixdofs/run.sh b/examples/features/geometry_optimization/SD_pswater_with_fixdofs/run.sh
@@ -0,0 +1,16 @@
+ipi=i-pi
+driver="i-pi-driver -m pswater -u -a h2o-geop"
+sleep_time=4
+
+${ipi} input.xml > log.i-pi & 
+echo "# i-PI is running"
+
+echo "# Waiting for ${sleep_time} (s) before executing driver"
+sleep ${sleep_time}
+
+${driver} > /dev/null & 
+echo "# Driver is running"
+
+wait
+
+echo "# Simulation complete"
diff --git a/ipi/engine/motion/geop.py b/ipi/engine/motion/geop.py
@@ -158,7 +158,8 @@ def bind(self, ens, beads, nm, cell, bforce, prng, omaker):
         # Binds optimizer
         self.optimizer.bind(self)
 
-        if len(self.fixatoms_dof) == len(self.beads[0]):
+        print("HERE", len(self.fixatoms_dof), len(self.beads[0]))
+        if len(self.fixatoms_dof) == 3 * len(self.beads[0]):
             softexit.trigger(
                 status="bad",
                 message="WARNING: all atoms are fixed, geometry won't change. Exiting simulation",

diff --git a/ipi/engine/motion/stringmep.py b/ipi/engine/motion/stringmep.py
@@ -424,7 +424,7 @@ def bind(self, ens, beads, nm, cell, bforce, prng, omaker):
                 else:
                     raise ValueError("Hessian size does not match system size.")
 
-        if len(self.fixatoms_dof // 3) == len(self.beads[0]):
+        if len(self.fixatoms_dof) == 3 * len(self.beads[0]):
             softexit.trigger(
                 status="bad",
                 message="WARNING: all atoms are fixed, geometry won't change. Exiting simulation.",