Stub of an o3-averaging example

docs/src/software/chemiscope.sec

@@ -17,3 +17,4 @@ repository <https://github.com/lab-cosmo/chemiscope>`_.
 - examples/pi-metad/pi-metad
 - examples/path-integrals/path-integrals
 - examples/thermostats/thermostats
+- examples/o3-averaging/o3-averaging

docs/src/software/i-pi.sec

@@ -12,3 +12,4 @@ it on the `ipi-code website <http://ipi-code.org>`_, the `documentation pages
 - examples/path-integrals/path-integrals
 - examples/pi-metad/pi-metad
 - examples/heat-capacity/heat-capacity
+- examples/o3-averaging/o3-averaging

docs/src/software/lammps.sec

@@ -10,3 +10,4 @@ efficient domain decomposition scheme. Learn more about LAMMPS on its `homepage
 - examples/thermostats/thermostats
 - examples/path-integrals/path-integrals
 - examples/heat-capacity/heat-capacity
+- examples/o3-averaging/o3-averaging

docs/src/topics/ml-models.sec

@@ -9,3 +9,4 @@ data.
 - examples/lode-linear/lode-linear
 - examples/sample-selection/sample-selection
 - examples/periodic-hamiltonian/periodic-hamiltonian
+- examples/o3-averaging/o3-averaging

docs/src/topics/sampling.sec

@@ -10,3 +10,4 @@ set of configurations of an atomistic system.
 - examples/pi-metad/pi-metad
 - examples/batch-cp2k/reference-trajectory
 - examples/heat-capacity/heat-capacity
+- examples/o3-averaging/o3-averaging

examples/o3-averaging/README.rst

@@ -0,0 +1,6 @@
+Rotational averaging of non-equivariant models
+==============================================
+
+This example shows how to assess (and to an extent correct) the 
+influence of non-equivariant terms in the potential energy computed
+by an unconstrained machine-learning model.

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

@@ -0,0 +1,35 @@
+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/in.lmp

@@ -0,0 +1,34 @@
+units		electron
+atom_style	full
+
+pair_style      lj/cut/tip4p/long 1 2 1 1 0.278072379 17.001
+# high-pppm precision and shift to get meaningful fd estimates
+kspace_style	pppm/tip4p 1e-5
+pair_modify     shift yes
+bond_style      class2
+angle_style     harmonic
+
+
+read_data	data/water_32_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

@@ -0,0 +1,5 @@
+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

@@ -0,0 +1,38 @@
+<!-- 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

@@ -0,0 +1,35 @@
+<!-- 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/input-noo3.xml

@@ -0,0 +1,41 @@
+<simulation verbosity='medium' safe_stride='100'>
+  <output prefix='water-noo3'>
+      <properties filename='out' stride='4'>  
+         [ step, time{picosecond}, conserved, potential, kinetic_cv, 
+           scaledcoords(fd_delta=5e-3) ] 
+      </properties>
+      <trajectory filename='noo3_pots' stride='2' extra_type="o3grid_pots"> extras_component_raw(1) </trajectory>  
+      <trajectory filename='pos' stride='20' format='ase'> positions </trajectory>
+  </output>
+  <total_steps> 2000 </total_steps>
+  <prng>
+    <seed> 32342 </seed>
+  </prng>
+  <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='pdb' units='angstrom'> data/water_32.pdb </file>
+      <velocities mode='thermal' units='kelvin'> 300 </velocities>
+    </initialize>
+    <forces>
+      <force forcefield='lmpserial'/>
+      <force forcefield='noo3'/>
+    </forces>
+    <ensemble>
+      <temperature units='kelvin'>300</temperature>
+    </ensemble>
+    <motion mode='dynamics'>
+      <dynamics mode='nvt'>
+        <thermostat mode='langevin'>
+          <tau units="femtosecond"> 100.0 </tau>     
+        </thermostat>
+        <timestep units='femtosecond'> 0.5 </timestep>
+      </dynamics>
+    </motion>
+  </system>
+</simulation>

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

@@ -0,0 +1,26 @@
+<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

@@ -0,0 +1,41 @@
+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

examples/o3-averaging/data/water_32.pdb

@@ -0,0 +1,98 @@
+CRYST1   10.260   10.260   10.260  90.00  90.00  90.00 P 1
+ATOM      1    O 1       1       3.756   4.710   9.494  0.00  0.00           O  
+ATOM      2    H 1       1       4.604   4.272   9.671  0.00  0.00           H  
+ATOM      3    H 1       1       3.998   5.320   8.788  0.00  0.00           H  
+ATOM      4    O 1       1       9.933   8.841   0.366  0.00  0.00           O  
+ATOM      5    H 1       1      10.132   8.196   1.120  0.00  0.00           H  
+ATOM      6    H 1       1       9.368   8.449  -0.316  0.00  0.00           H  
+ATOM      7    O 1       1       0.321   1.492   5.796  0.00  0.00           O  
+ATOM      8    H 1       1      -0.287   1.993   5.241  0.00  0.00           H  
+ATOM      9    H 1       1       0.791   2.061   6.364  0.00  0.00           H  
+ATOM     10    O 1       1       8.035   9.735   4.307  0.00  0.00           O  
+ATOM     11    H 1       1       7.203   9.789   4.847  0.00  0.00           H  
+ATOM     12    H 1       1       8.636   9.307   4.920  0.00  0.00           H  
+ATOM     13    O 1       1       5.663   9.082   0.660  0.00  0.00           O  
+ATOM     14    H 1       1       6.378   9.721   0.814  0.00  0.00           H  
+ATOM     15    H 1       1       5.213   8.991   1.552  0.00  0.00           H  
+ATOM     16    O 1       1       8.130   0.215   1.201  0.00  0.00           O  
+ATOM     17    H 1       1       8.196  -0.065   2.118  0.00  0.00           H  
+ATOM     18    H 1       1       8.938  -0.161   0.818  0.00  0.00           H  
+ATOM     19    O 1       1       8.177   4.165   0.716  0.00  0.00           O  
+ATOM     20    H 1       1       7.895   5.066   0.840  0.00  0.00           H  
+ATOM     21    H 1       1       7.722   3.562   1.341  0.00  0.00           H  
+ATOM     22    O 1       1       6.341   3.256   9.678  0.00  0.00           O  
+ATOM     23    H 1       1       7.133   3.423  10.189  0.00  0.00           H  
+ATOM     24    H 1       1       6.507   2.398   9.350  0.00  0.00           H  
+ATOM     25    O 1       1       0.136   7.798   2.738  0.00  0.00           O  
+ATOM     26    H 1       1      -0.006   8.300   3.584  0.00  0.00           H  
+ATOM     27    H 1       1       0.314   6.905   2.966  0.00  0.00           H  
+ATOM     28    O 1       1       5.027   2.563   6.169  0.00  0.00           O  
+ATOM     29    H 1       1       5.538   3.336   6.262  0.00  0.00           H  
+ATOM     30    H 1       1       5.313   2.031   6.922  0.00  0.00           H  
+ATOM     31    O 1       1       7.164   2.542   2.418  0.00  0.00           O  
+ATOM     32    H 1       1       6.248   2.467   2.667  0.00  0.00           H  
+ATOM     33    H 1       1       7.384   1.681   2.057  0.00  0.00           H  
+ATOM     34    O 1       1       3.336   9.051   3.265  0.00  0.00           O  
+ATOM     35    H 1       1       2.818   8.341   2.787  0.00  0.00           H  
+ATOM     36    H 1       1       2.733   9.794   3.398  0.00  0.00           H  
+ATOM     37    O 1       1       1.476   1.420   0.819  0.00  0.00           O  
+ATOM     38    H 1       1       1.060   0.568   0.631  0.00  0.00           H  
+ATOM     39    H 1       1       1.582   1.509   1.770  0.00  0.00           H  
+ATOM     40    O 1       1       1.222   4.946   3.218  0.00  0.00           O  
+ATOM     41    H 1       1       2.111   4.703   3.522  0.00  0.00           H  
+ATOM     42    H 1       1       1.342   4.956   2.245  0.00  0.00           H  
+ATOM     43    O 1       1       6.790   6.491   4.488  0.00  0.00           O  
+ATOM     44    H 1       1       7.083   5.755   5.074  0.00  0.00           H  
+ATOM     45    H 1       1       6.747   7.293   4.975  0.00  0.00           H  
+ATOM     46    O 1       1       9.330   3.465   4.430  0.00  0.00           O  
+ATOM     47    H 1       1       9.974   3.956   3.918  0.00  0.00           H  
+ATOM     48    H 1       1       8.583   3.143   3.966  0.00  0.00           H  
+ATOM     49    O 1       1       7.484   4.543   6.379  0.00  0.00           O  
+ATOM     50    H 1       1       7.604   4.450   7.328  0.00  0.00           H  
+ATOM     51    H 1       1       8.241   4.098   5.987  0.00  0.00           H  
+ATOM     52    O 1       1       0.448   5.701   8.219  0.00  0.00           O  
+ATOM     53    H 1       1       0.573   4.840   7.871  0.00  0.00           H  
+ATOM     54    H 1       1       0.720   5.651   9.123  0.00  0.00           H  
+ATOM     55    O 1       1       0.736   4.082   0.545  0.00  0.00           O  
+ATOM     56    H 1       1       1.032   3.147   0.501  0.00  0.00           H  
+ATOM     57    H 1       1      -0.250   3.978   0.476  0.00  0.00           H  
+ATOM     58    O 1       1       4.229   2.582   3.562  0.00  0.00           O  
+ATOM     59    H 1       1       4.650   2.364   4.424  0.00  0.00           H  
+ATOM     60    H 1       1       4.306   3.526   3.496  0.00  0.00           H  
+ATOM     61    O 1       1       3.749   5.318   3.591  0.00  0.00           O  
+ATOM     62    H 1       1       3.577   5.600   2.690  0.00  0.00           H  
+ATOM     63    H 1       1       4.519   5.812   3.831  0.00  0.00           H  
+ATOM     64    O 1       1       0.242   8.540   5.195  0.00  0.00           O  
+ATOM     65    H 1       1       0.243   9.452   5.454  0.00  0.00           H  
+ATOM     66    H 1       1       0.725   8.102   5.864  0.00  0.00           H  
+ATOM     67    O 1       1       6.065   0.243   8.171  0.00  0.00           O  
+ATOM     68    H 1       1       6.685  -0.360   8.559  0.00  0.00           H  
+ATOM     69    H 1       1       5.235  -0.020   8.586  0.00  0.00           H  
+ATOM     70    O 1       1       7.362   8.029   9.049  0.00  0.00           O  
+ATOM     71    H 1       1       6.719   7.831   8.312  0.00  0.00           H  
+ATOM     72    H 1       1       6.813   7.839   9.757  0.00  0.00           H  
+ATOM     73    O 1       1       1.971   1.171   3.631  0.00  0.00           O  
+ATOM     74    H 1       1       1.520   1.399   4.474  0.00  0.00           H  
+ATOM     75    H 1       1       2.821   1.577   3.533  0.00  0.00           H  
+ATOM     76    O 1       1       7.674   6.605   2.134  0.00  0.00           O  
+ATOM     77    H 1       1       7.143   6.490   2.918  0.00  0.00           H  
+ATOM     78    H 1       1       8.563   6.681   2.409  0.00  0.00           H  
+ATOM     79    O 1       1       2.769   7.384   7.275  0.00  0.00           O  
+ATOM     80    H 1       1       2.353   8.088   7.748  0.00  0.00           H  
+ATOM     81    H 1       1       2.249   6.554   7.408  0.00  0.00           H  
+ATOM     82    O 1       1       2.253   2.791   7.349  0.00  0.00           O  
+ATOM     83    H 1       1       2.718   3.230   8.076  0.00  0.00           H  
+ATOM     84    H 1       1       2.955   2.671   6.707  0.00  0.00           H  
+ATOM     85    O 1       1       3.652   9.953   9.290  0.00  0.00           O  
+ATOM     86    H 1       1       4.114   9.509   9.983  0.00  0.00           H  
+ATOM     87    H 1       1       3.199  10.639   9.784  0.00  0.00           H  
+ATOM     88    O 1       1       5.263   6.708   7.589  0.00  0.00           O  
+ATOM     89    H 1       1       4.318   7.082   7.707  0.00  0.00           H  
+ATOM     90    H 1       1       5.455   7.057   6.733  0.00  0.00           H  
+ATOM     91    O 1       1       3.507   6.721   1.020  0.00  0.00           O  
+ATOM     92    H 1       1       4.097   7.303   0.607  0.00  0.00           H  
+ATOM     93    H 1       1       3.586   5.984   0.419  0.00  0.00           H  
+ATOM     94    O 1       1       5.455   9.196   5.888  0.00  0.00           O  
+ATOM     95    H 1       1       5.473   9.602   6.758  0.00  0.00           H  
+ATOM     96    H 1       1       4.549   9.238   5.484  0.00  0.00           H  
+END