Make some progress

examples/o3-averaging/data/in-mol.lmp

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+units		electron
+atom_style	full
+
+pair_style      lj/cut/tip4p/cut 1 2 1 1 0.278072379 17.001
+# high-pppm precision and shift to get meaningful fd estimates
+# kspace_style	none
+# kspace_style	pppm/tip4p 1e-5
+pair_modify     shift yes
+bond_style      class2
+angle_style     harmonic
+
+
+read_data	water_1_data.lmp
+pair_coeff  * * 0 0
+pair_coeff  1  1  0.000295147 5.96946
+
+neighbor	2.0 bin
+
+
+timestep	0.00025
+
+#velocity all create 298.0 2345187
+
+#thermo_style	multi
+#thermo		1
+
+#fix		1 all nvt temp 298.0 298.0 30.0 tchain 1
+#fix 1 all nve
+fix 1 all ipi h2o-lammps 32342 unix
+
+
+#dump		1 all xyz 25 dump.xyz
+
+run		100000000
+

examples/o3-averaging/data/init-mol.xyz

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+3
+Lattice="100.0 0.0 0.0 0.0 100.0 0.0 0.0 0.0 100.0" Properties=species:S:1:pos:R:3:momenta:R:3 ipi_comment="Step:      200000  Bead:       0 positions{angstrom}  cell{angstrom}" pbc="T T T"
+O       -2.89770838       6.76492149      25.78733892       0.41094839      -0.09429088       0.29861888
+H       -3.22693259       6.92327461      24.89600383      -0.31547195       0.04597911      -0.02131858
+H       -3.73951469       6.82619967      26.21403556      -0.09547645       0.04831177      -0.27730030

examples/o3-averaging/data/input-mol-grid.xml

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+<!-- safe_stride is the frequency at which i-PI makes internal snapshots for restarting -->
+<simulation verbosity='medium' threading='false' safe_stride='10'>
+    <ffsocket name='lmpserial' mode='unix' pbc='false'>
+      <address>h2o-lammps</address> <latency> 1e-4 </latency>
+    </ffsocket>
+   <ffrotations name='driver-noo3' mode='unix' pbc='false'>
+       <address>h2o-noo3</address>
+       <grid_order> 3 </grid_order>
+       <grid_mode> legendre </grid_mode>
+       <inversion> True </inversion>
+   </ffrotations>
+   <total_steps>10000</total_steps>
+   <output prefix='nve-mol'>
+      <trajectory stride='20' filename='pos' format='xyz'> positions </trajectory>
+      <properties stride='20'> [ step, time, conserved, temperature{kelvin}, kinetic_md, potential, pressure_md ] </properties>
+   </output>
+   <prng>
+      <seed>32123</seed>
+   </prng>
+   <system>
+      <forces> 
+          <force forcefield='lmpserial'></force>
+          <force forcefield='driver-noo3' weight="1.0"/>
+      </forces>
+      <initialize nbeads='1'>
+        <file mode='ase'> init-mol.xyz </file>
+      </initialize>
+      <ensemble>
+         <temperature units='kelvin'> 300 </temperature>
+      </ensemble>
+      <motion mode='dynamics'>
+        <fixcom> True </fixcom>
+        <dynamics mode='nve'>
+            <timestep units='femtosecond'> 0.5 </timestep>
+        </dynamics>
+      </motion>
+  </system>
+</simulation>

examples/o3-averaging/data/input-mol-noo3.xml

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+<!-- safe_stride is the frequency at which i-PI makes internal snapshots for restarting -->
+<simulation verbosity='medium' threading='false' safe_stride='10'>
+    <ffsocket name='lmpserial' mode='unix' pbc='false'>
+      <address>h2o-lammps</address> <latency> 1e-4 </latency>
+    </ffsocket>
+   <ffsocket name='driver-noo3' mode='unix' pbc='false'>
+       <address>h2o-noo3</address>
+   </ffsocket>
+   <total_steps>10000</total_steps>
+   <output prefix='nve-mol'>
+      <trajectory stride='20' filename='pos' format='xyz'> positions </trajectory>
+      <properties stride='20'> [ step, time, conserved, temperature{kelvin}, kinetic_md, potential, pressure_md ] </properties>
+   </output>
+   <prng>
+      <seed>32123</seed>
+   </prng>
+   <system>
+      <forces> 
+          <force forcefield='lmpserial'></force>
+          <force forcefield='driver-noo3' weight="1.0"/>
+      </forces>
+      <initialize nbeads='1'>
+        <file mode='ase'> init-mol.xyz </file>
+      </initialize>
+      <ensemble>
+         <temperature units='kelvin'> 300 </temperature>
+      </ensemble>
+      <motion mode='dynamics'>
+        <fixcom> True </fixcom>
+        <dynamics mode='nve'>
+            <timestep units='femtosecond'> 0.5 </timestep>
+        </dynamics>
+      </motion>
+  </system>
+</simulation>

examples/o3-averaging/data/replay-noo3.xml

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+<simulation verbosity='medium' safe_stride='100'>
+  <output prefix='water-noo3'>
+      <properties filename='out' stride='1'>  
+         [ step, time{picosecond}, conserved, potential, kinetic_cv, 
+           scaledcoords(fd_delta=5e-3) ] 
+      </properties>
+  </output>
+  <ffsocket name='lmpserial' mode='unix' pbc='false'>
+      <address>h2o-lammps</address> <latency> 1e-4 </latency>
+  </ffsocket>
+  <ffrotations name='noo3' mode='unix' pbc='false'>
+      <address>h2o-noo3</address> <latency> 1e-4 </latency>
+  </ffrotations>
+  <system>
+    <initialize nbeads='1'>
+      <file mode='ase' units='angstrom'> init-mol.xyz </file>
+    </initialize>
+    <forces>
+      <force forcefield='lmpserial'/>
+      <force forcefield='noo3'/>
+    </forces>
+    <motion mode='replay'>
+      <file mode='ase'> replay.xyz </file>
+    </motion>
+  </system>
+</simulation>

examples/o3-averaging/data/water_1_data.lmp

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+LAMMPS Description
+
+         3  atoms
+         2  bonds
+         1  angles
+
+           2  atom types
+           1  bond types
+           1  angle types
+
+         -19 19.38859 xlo xhi
+         -10 19.38859 ylo yhi
+         -19 19.38859 zlo zhi
+
+Masses
+
+  1 15.9994
+  2  1.0080
+
+Bond Coeffs
+
+  1    1.78    0.2708585 -0.327738785 0.231328959
+
+Angle Coeffs
+
+  1    0.0700  107.400000
+
+Atoms
+
+  1 1 1 -1.1128        7.098  8.901  17.941  
+  2 1 2 0.5564         8.700  8.073  18.276  
+  3 1 2 0.5564         7.555  10.053  16.607 
+
+Bonds
+
+ 1 1 1 2
+ 2 1 1 3
+
+Angles
+
+ 1 1 2 1 3