Environment similarity collective variable (plumed#562)

* First commit

* Input ref environments from PDB files and clean up

* Fixed errors in compilation

* Encapsulated parsinf of ref envs in function

* Fixed problem with maxDistance function

* Add regtests - derivatives missing

* Add regtest for derivatives

* Update citation

* Add regtest for DIAMOND option

* Documentation of EnvironmentSimilarity

* Add link to Environment Finder

* Update docs and fix virial

* Remove old file

* Fix namespace issue; fix LGTM alert

regtest/crystallization/rt-env-sim/rt-bcc/COLVAR.reference

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+#! FIELDS time es.mean es.morethan
+ 0.000000 1.001178 249.939835

regtest/crystallization/rt-env-sim/rt-bcc/Makefile

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+include ../../../scripts/test.make

regtest/crystallization/rt-env-sim/rt-bcc/config

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+type=driver
+plumed_modules=crystallization
+# this is to test a different name
+arg="--plumed plumed.dat --mf_pdb bcc.pdb"

regtest/crystallization/rt-env-sim/rt-bcc/plumed.dat

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+# vim:ft=plumed
+
+ENVIRONMENTSIMILARITY ...
+ SPECIES=1-250
+ SIGMA=0.065
+ LATTICE_CONSTANTS=0.4234
+ CRYSTAL_STRUCTURE=BCC
+ LABEL=es
+ MEAN
+ MORE_THAN={RATIONAL R_0=0.5 NN=12 MM=24}
+... ENVIRONMENTSIMILARITY
+
+PRINT ARG=es.mean,es.morethan FILE=COLVAR STRIDE=1
+

regtest/crystallization/rt-env-sim/rt-custom-1env/COLVAR.reference

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+#! FIELDS time es.mean es.morethan
+ 0.000000 0.319486 24.000529

regtest/crystallization/rt-env-sim/rt-custom-1env/Makefile

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+include ../../../scripts/test.make

regtest/crystallization/rt-env-sim/rt-custom-1env/config

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+type=driver
+plumed_modules=crystallization
+# this is to test a different name
+arg="--plumed plumed.dat --mf_pdb IceIh.pdb"

regtest/crystallization/rt-env-sim/rt-custom-1env/env1.pdb

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+ATOM      1    O MOL     1      -2.239  -1.296  -0.917  1.00  0.00           O  
+ATOM      2    O MOL     1       0.000   0.000   2.751  1.00  0.00           O  
+ATOM      3    O MOL     1       0.000   2.594  -0.917  1.00  0.00           O  
+ATOM      4    O MOL     1       2.246  -1.296  -0.917  1.00  0.00           O  

regtest/crystallization/rt-env-sim/rt-custom-1env/plumed.dat

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+# vim:ft=plumed
+
+ENVIRONMENTSIMILARITY ...
+ SPECIES=1-288:3
+ SIGMA=0.05
+ CRYSTAL_STRUCTURE=CUSTOM
+ REFERENCE=env1.pdb
+ LABEL=es
+ MEAN
+ MORE_THAN={RATIONAL R_0=0.5 NN=12 MM=24}
+... ENVIRONMENTSIMILARITY
+
+PRINT ARG=es.mean,es.morethan FILE=COLVAR STRIDE=1
+

regtest/crystallization/rt-env-sim/rt-custom-multienv/COLVAR.reference

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+#! FIELDS time es.mean es.morethan
+ 0.000000 0.999991 95.976566

regtest/crystallization/rt-env-sim/rt-custom-multienv/Makefile

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+include ../../../scripts/test.make

regtest/crystallization/rt-env-sim/rt-custom-multienv/config

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+type=driver
+plumed_modules=crystallization
+# this is to test a different name
+arg="--plumed plumed.dat --mf_pdb IceIh.pdb"

regtest/crystallization/rt-env-sim/rt-custom-multienv/env1.pdb

@@ -0,0 +1,4 @@
+ATOM      1    O MOL     1      -2.239  -1.296  -0.917  1.00  0.00           O  
+ATOM      2    O MOL     1       0.000   0.000   2.751  1.00  0.00           O  
+ATOM      3    O MOL     1       0.000   2.594  -0.917  1.00  0.00           O  
+ATOM      4    O MOL     1       2.246  -1.296  -0.917  1.00  0.00           O  

regtest/crystallization/rt-env-sim/rt-custom-multienv/env2.pdb

@@ -0,0 +1,4 @@
+ATOM      1    O MOL     1      -2.239   1.297  -0.917  1.00  0.00           O  
+ATOM      2    O MOL     1       0.000  -2.594  -0.917  1.00  0.00           O  
+ATOM      3    O MOL     1       0.000   0.000   2.751  1.00  0.00           O  
+ATOM      4    O MOL     1       2.246   1.297  -0.917  1.00  0.00           O  

regtest/crystallization/rt-env-sim/rt-custom-multienv/env3.pdb

@@ -0,0 +1,4 @@
+ATOM      1    O MOL     1      -2.246   1.296   0.917  1.00  0.00           O  
+ATOM      2    O MOL     1       0.000  -2.594   0.917  1.00  0.00           O  
+ATOM      3    O MOL     1       0.000   0.000  -2.751  1.00  0.00           O  
+ATOM      4    O MOL     1       2.246   1.296   0.917  1.00  0.00           O  

regtest/crystallization/rt-env-sim/rt-custom-multienv/env4.pdb

@@ -0,0 +1,4 @@
+ATOM      1    O MOL     1      -2.246  -1.297   0.917  1.00  0.00           O  
+ATOM      2    O MOL     1       0.000   0.000  -2.751  1.00  0.00           O  
+ATOM      3    O MOL     1       0.000   2.594   0.917  1.00  0.00           O  
+ATOM      4    O MOL     1       2.246  -1.297   0.917  1.00  0.00           O  

regtest/crystallization/rt-env-sim/rt-custom-multienv/plumed.dat

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+# vim:ft=plumed
+
+ENVIRONMENTSIMILARITY ...
+ SPECIES=1-288:3
+ SIGMA=0.05
+ CRYSTAL_STRUCTURE=CUSTOM
+ REFERENCE_1=env1.pdb
+ REFERENCE_2=env2.pdb
+ REFERENCE_3=env3.pdb
+ REFERENCE_4=env4.pdb
+ LABEL=es
+ MEAN
+ MORE_THAN={RATIONAL R_0=0.5 NN=12 MM=24}
+... ENVIRONMENTSIMILARITY
+
+PRINT ARG=es.mean,es.morethan FILE=COLVAR STRIDE=1
+

regtest/crystallization/rt-env-sim/rt-deriv-multienv/Makefile

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+include ../../../scripts/test.make

regtest/crystallization/rt-env-sim/rt-deriv-multienv/config

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+type=driver
+plumed_modules=crystallization
+# this is to test a different name
+arg="--plumed plumed.dat --mf_pdb IceIh.pdb"