add folders

Author: DavideTisi

examples/free-energy/geop/init.xyz

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+1
+# CELL(GENH): 100.0 0.0 0.0 0.0 100.0 0.0 0.0 0.0 100.0 positions{angstrom} cell{angstrom}
+H 2.0 0.2 -0.5 

examples/free-energy/geop/input.xml

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+<simulation mode='static' verbosity='high'>
+  <output prefix='geop'>
+    <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='driver' mode='unix' pbc='false'>
+    <address> geop </address>
+  </ffsocket>
+  <system>
+    <initialize nbeads='1'>
+      <file mode='xyz'> geop/init.xyz </file>
+    </initialize>
+    <forces>
+      <force forcefield='driver'> </force>
+    </forces>
+    <motion mode='minimize'>
+      <optimizer mode='bfgs'>
+        <tolerances>
+          <energy> 1e-5 </energy>
+          <force> 1e-5 </force>
+          <position> 1e-5 </position>
+        </tolerances>
+      </optimizer>
+    </motion>
+  </system>
+</simulation>

examples/free-energy/harm/input.xml

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+<simulation mode='static' verbosity='high'>
+  <output prefix='harm'>
+    <properties stride='10' filename='out'>  [ step, potential ] </properties>
+  </output>
+  <total_steps> 5000 </total_steps>
+  <prng>
+    <seed> 32342 </seed>
+  </prng>
+  <ffsocket name='lmp' mode='unix' pbc='true'>
+    <address> vib </address>
+  </ffsocket>
+  <system>
+    <initialize nbeads='1'>
+      <file mode='ase'> init_harm.xyz </file>
+    </initialize>
+    <forces>
+      <force forcefield='lmp'> </force>
+    </forces>
+    <motion mode='vibrations'>
+      <vibrations mode='fd'>
+        <pos_shift> 0.001 </pos_shift>
+        <prefix> phonons </prefix>
+        <asr> none </asr>
+      </vibrations>
+    </motion>
+  </system>
+</simulation>