Add PDI Sampling Unit Tests

[RainierBarrett]

This adds some basic unit tests for checking PDI functionality. For some reason, git didn't detect that I only changed part of the upstream file when merging.

[RainierBarrett]

Updated the tests as requested. Mysteriously, I now get inconsistent behavior from pytest, where if I run all tests in test_systems.py, I get one failed test, test_gauss_dist, saying PACKMOL failed. But when I run it with -k test_gauss_dist it passes. It seems like the box is out of room, but I have no idea why it doesn't throw this when I run the single test... Here's the log:

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PACKMOL - Packing optimization for the automated generation of starting configurations for molecular dynamics simulations.

                                                          Version 18.169 

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Packmol must be run with: packmol < inputfile.inp

Userguide at: www.ime.unicamp.br/~martinez/packmol

Reading input file... (Control-C aborts) User set maximum system dimensions: 1000.0000000000000
Seed for random number generator: 12345 Output file: /tmp/tmpefr__uj2.xyz Reading coordinate file: /tmp/tmppr07oshv.xyz Reading coordinate file: /tmp/tmp7wge2jqh.xyz Reading coordinate file: /tmp/tmpefngnn7d.xyz Reading coordinate file: /tmp/tmps1pwyxhm.xyz Reading coordinate file: /tmp/tmp5fxwqjj2.xyz Number of independent structures: 5 The structures are: Structure 1 :/tmp/tmppr07oshv.xyz - created by mBuild( 36 atoms) Structure 2 :/tmp/tmp7wge2jqh.xyz - created by mBuild( 206 atoms) Structure 3 :/tmp/tmpefngnn7d.xyz - created by mBuild( 342 atoms) Structure 4 :/tmp/tmps1pwyxhm.xyz - created by mBuild( 478 atoms) Structure 5 :/tmp/tmp5fxwqjj2.xyz - created by mBuild( 1434 atoms) Maximum number of GENCAN loops for all molecule packing: 1000 Total number of restrictions: 5 Distance tolerance: 2.0000000000000000
Number of molecules of type 1 : 1 Number of molecules of type 2 : 1 Number of molecules of type 3 : 1 Number of molecules of type 4 : 1 Number of molecules of type 5 : 1 Total number of atoms: 2496 Total number of molecules: 5 Number of fixed molecules: 0 Number of free molecules: 5 Number of variables: 30 Total number of fixed atoms: 0 Rotations about x axis of molecules of type 1 will be constrained. Rotations about y axis of molecules of type 1 will be constrained. Rotations about z axis of molecules of type 1 will be constrained. Rotations about x axis of molecules of type 2 will be constrained. Rotations about y axis of molecules of type 2 will be constrained. Rotations about z axis of molecules of type 2 will be constrained. Rotations about x axis of molecules of type 3 will be constrained. Rotations about y axis of molecules of type 3 will be constrained. Rotations about z axis of molecules of type 3 will be constrained. Rotations about x axis of molecules of type 4 will be constrained. Rotations about y axis of molecules of type 4 will be constrained. Rotations about z axis of molecules of type 4 will be constrained. Rotations about x axis of molecules of type 5 will be constrained. Rotations about y axis of molecules of type 5 will be constrained. Rotations about z axis of molecules of type 5 will be constrained. Maximum internal distance of type 1 : 13.138706439628750
Maximum internal distance of type 2 : 58.705157228339054
Maximum internal distance of type 3 : 76.672020272637766
Maximum internal distance of type 4 : 107.49875529471331
Maximum internal distance of type 5 : 309.37499688405626
All atoms must be within these coordinates: x: [ -988.50847543440159 , 1011.4915245655984 ] y: [ -992.85047540958760 , 1007.1495245904124 ] z: [ -987.20000000000005 , 1012.8000000000000 ] If the system is larger than this, increase the sidemax parameter.

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Building initial approximation ...

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Adjusting initial point to fit the constraints

---

---

Molecules of type: 1

Packing:|0 100%| |**

Restraint-only function value: 0.0000000000000000
Maximum violation of the restraints: 0.0000000000000000

---

Molecules of type: 2

Packing:|0 100%| |****

Restraint-only function value: 3.1409452725247351E-022 Maximum violation of the restraints: 3.1409452725247351E-022

---

Molecules of type: 3

Packing:|0 100%| |**|

Restraint-only function value: 0.0000000000000000
Maximum violation of the restraints: 0.0000000000000000

---

Molecules of type: 4

Packing:|0 100%| |****

Restraint-only function value: 4.8335005110216120E-020 Maximum violation of the restraints: 3.8180867812696971E-020

---

Molecules of type: 5

Packing:	0 100%		**** Fixing bad orientations ... 1 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155203 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155211 Packing:	0 100%

Fixing bad orientations ... 2 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155211 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155188 Packing:	0 100%

Fixing bad orientations ... 3 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155188 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155179 Packing:	0 100%

Fixing bad orientations ... 4 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155179 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155188 Packing:	0 100%

Fixing bad orientations ... 5 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155188 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155203 Packing:	0 100%

Fixing bad orientations ... 6 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155203 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155197 Packing:	0 100%

Fixing bad orientations ... 7 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155197 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155188 Packing:	0 100%

Fixing bad orientations ... 8 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155188 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155211 Packing:	0 100%

Fixing bad orientations ... 9 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155211 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155223 Packing:	0 100%

Fixing bad orientations ... 10 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155223 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155203 Packing:	0 100%

Fixing bad orientations ... 11 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155203 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155162 Packing:	0 100%

Fixing bad orientations ... 12 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155162 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155185 Packing:	0 100%

Fixing bad orientations ... 13 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155185 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155179 Packing:	0 100%

Fixing bad orientations ... 14 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155179 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155203 Packing:	0 100%

Fixing bad orientations ... 15 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155203 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155203 Packing:	0 100%

Fixing bad orientations ... 16 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155203 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155182 Packing:	0 100%

Fixing bad orientations ... 17 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155182 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155194 Packing:	0 100%

Fixing bad orientations ... 18 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155194 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155194 Packing:	0 100%

Fixing bad orientations ... 19 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155194 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155211 Packing:	0 100%

Fixing bad orientations ... 20 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155211 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155203 Packing:	0 100%

Fixing bad orientations ... 21 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155203 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155197 Packing:	0 100%

Fixing bad orientations ... 22 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155197 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155197 Packing:	0 100%

Fixing bad orientations ... 23 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155197 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155217 Packing:	0 100%

Fixing bad orientations ... 24 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155217 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155191 Packing:	0 100%

Fixing bad orientations ... 25 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155191 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155171 Packing:	0 100%

Fixing bad orientations ... 26 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155171 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155165 Packing:	0 100%

Fixing bad orientations ... 27 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155165 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155177 Packing:	0 100%

Fixing bad orientations ... 28 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155177 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155211 Packing:	0 100%

Fixing bad orientations ... 29 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155211 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155217 Packing:	0 100%

Fixing bad orientations ... 30 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155217 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155206 Packing:	0 100%

Fixing bad orientations ... 31 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155206 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155200 Packing:	0 100%

Fixing bad orientations ... 32 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155200 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155185 Packing:	0 100%

Fixing bad orientations ... 33 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155185 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155168 Packing:	0 100%

Fixing bad orientations ... 34 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155168 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155174 Packing:	0 100%

Fixing bad orientations ... 35 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155174 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155214 Packing:	0 100%

Fixing bad orientations ... 36 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155214 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155185 Packing:	0 100%

Fixing bad orientations ... 37 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155185 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155179 Packing:	0 100%

Fixing bad orientations ... 38 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155179 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155209 Packing:	0 100%

Fixing bad orientations ... 39 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155209 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155203 Packing:	0 100%

Fixing bad orientations ... 40 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155203 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155206 Packing:	0 100%

Fixing bad orientations ... 41 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155206 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155188 Packing:	0 100%

Fixing bad orientations ... 42 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155188 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155188 Packing:	0 100%

Fixing bad orientations ... 43 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155188 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155209 Packing:	0 100%

Fixing bad orientations ... 44 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155209 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155211 Packing:	0 100%

Fixing bad orientations ... 45 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155211 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155197 Packing:	0 100%

Fixing bad orientations ... 46 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155197 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155188 Packing:	0 100%

Fixing bad orientations ... 47 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155188 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155156 Packing:	0 100%

Fixing bad orientations ... 48 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155156 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155214 Packing:	0 100%

Fixing bad orientations ... 49 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155214 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155197 Packing:	0 100%

Fixing bad orientations ... 50 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155197 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155200 Packing:	0 100%

Fixing bad orientations ... 51 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155200 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155171 Packing:	0 100%

Fixing bad orientations ... 52 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155171 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155209 Packing:	0 100%

Fixing bad orientations ... 53 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155209 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155179 Packing:	0 100%

Fixing bad orientations ... 54 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155179 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155194 Packing:	0 100%

Fixing bad orientations ... 55 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155194 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155188 Packing:	0 100%

Fixing bad orientations ... 56 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155188 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155179 Packing:	0 100%		*** Fixing bad orientations ... 57 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155174 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155179 Packing:	0 100%

Fixing bad orientations ... 58 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155179 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155209 Packing:	0 100%

Fixing bad orientations ... 59 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155209 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155197 Packing:	0 100%

Fixing bad orientations ... 60 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155197 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155188 Packing:	0 100%

Fixing bad orientations ... 61 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155188 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155191 Packing:	0 100%

Fixing bad orientations ... 62 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155191 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155211 Packing:	0 100%

Fixing bad orientations ... 63 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155211 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155211 Packing:	0 100%

Fixing bad orientations ... 64 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155211 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155191 Packing:	0 100%

Fixing bad orientations ... 65 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155191 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155197 Packing:	0 100%

Fixing bad orientations ... 66 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155197 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155203 Packing:	0 100%

Fixing bad orientations ... 67 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155203 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155185 Packing:	0 100%

Fixing bad orientations ... 68 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155185 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155185 Packing:	0 100%

Fixing bad orientations ... 69 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155185 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155211 Packing:	0 100%

Fixing bad orientations ... 70 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155211 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155188 Packing:	0 100%		*** Fixing bad orientations ... 71 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155171 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155211 Packing:	0 100%

Fixing bad orientations ... 72 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155211 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155206 Packing:	0 100%

Fixing bad orientations ... 73 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155206 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155206 Packing:	0 100%

Fixing bad orientations ... 74 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155206 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155179 Packing:	0 100%

Fixing bad orientations ... 75 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155179 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155168 Packing:	0 100%

Fixing bad orientations ... 76 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155168 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155206 Packing:	0 100%

Fixing bad orientations ... 77 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155206 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155211 Packing:	0 100%

Fixing bad orientations ... 78 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155211 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155217 Packing:	0 100%

Fixing bad orientations ... 79 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155217 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155194 Packing:	0 100%

Fixing bad orientations ... 80 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155194 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155200 Packing:	0 100%

Fixing bad orientations ... 81 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155200 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155182 Packing:	0 100%

Fixing bad orientations ... 82 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155182 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155197 Packing:	0 100%

Fixing bad orientations ... 83 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155197 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155214 Packing:	0 100%

Fixing bad orientations ... 84 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155214 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155197 Packing:	0 100%

Fixing bad orientations ... 85 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155197 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155206 Packing:	0 100%

Fixing bad orientations ... 86 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155206 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155203 Packing:	0 100%

Fixing bad orientations ... 87 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155203 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155191 Packing:	0 100%

Fixing bad orientations ... 88 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155191 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155200 Packing:	0 100%

Fixing bad orientations ... 89 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155200 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155209 Packing:	0 100%

Fixing bad orientations ... 90 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155209 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155223 Packing:	0 100%

Fixing bad orientations ... 91 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155223 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155200 Packing:	0 100%

Fixing bad orientations ... 92 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155200 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155217 Packing:	0 100%

Fixing bad orientations ... 93 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155217 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155200 Packing:	0 100%

Fixing bad orientations ... 94 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155200 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155182 Packing:	0 100%

Fixing bad orientations ... 95 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155182 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155179 Packing:	0 100%		*** Fixing bad orientations ... 96 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155174 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155226 Packing:	0 100%

Fixing bad orientations ... 97 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155226 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155209 Packing:	0 100%

Fixing bad orientations ... 98 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155209 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155156 Packing:	0 100%

Fixing bad orientations ... 99 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155156 Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:	0 100%		**	Function value after moving molecules: 211053.27233155188 Packing:	0 100%

Fixing bad orientations ... 100 of 100 Moving worst molecules ... Function value before moving molecules: 211053.27233155188
Type 5 molecules with non-zero contributions: 100.00% Moving 1 molecules of type 5 New positions will be based on good molecules (movebadrandom is not set) Moving:|0 100%| |**| Function value after moving molecules: 211053.27233155165

Restraint-only function value: 211053.27233155165
Maximum violation of the restraints: 2311.8016614979847
ERROR: Packmol was unable to put the molecules in the desired regions even without considering distance tolerances. Probably there is something wrong with the constraints, since it seems that the molecules cannot satisfy them at at all. Please check the spatial constraints and try again.

The maximum number of cycles ( 100 ) was achieved. You may try increasing it with the nloop0 keyword, as in: nloop0 1000

[jennyfothergill]

let's pull the new testing changes into this branch so we can see if the tests pass in the container

[codecov[bot]]

Codecov Report

Merging #27 (402dfdc) into master (d60f7a5) will increase coverage by 1.16%. The diff coverage is n/a.

@@            Coverage Diff             @@
##           master      #27      +/-   ##
==========================================
+ Coverage   81.70%   82.87%   +1.16%     
==========================================
  Files          11        6       -5     
  Lines         503      438      -65     
==========================================
- Hits          411      363      -48     
+ Misses         92       75      -17     

Impacted Files	Coverage Δ
uli_init/__version__.py
uli_init/compounds/__init__.py
uli_init/forcefields/__init__.py
uli_init/tests/base_test.py
uli_init/tests/test_simulations.py
uli_init/utils/unit_conversions.py	0.00% <0.00%> (ø)
uli_init/simulate.py	94.39% <0.00%> (+10.02%)	:arrow_up:

[jennyfothergill]

OK, all tests passing 🎉 One suggestion: right now the gaussian distribution test is run with 3 members, which kind of doesn't make sense for testing a distribution. Eventually it might be nice to add a larger test for _recover_mass_dist() function and checking that the returned distribution dictionary does match the specified distribution.