provide reference logfiles and move generated files to reference folder

2018-11-02 23:28:09 -04:00
parent 18216de084
commit ac11d66d5a
4 changed files with 324 additions and 0 deletions
--- a/examples/USER/plumed/reference/p.log
+++ b/examples/USER/plumed/reference/p.log
@ -0,0 +1,57 @@
+PLUMED: PLUMED is starting
+PLUMED: Version: 2.4.2 (git: Unknown) compiled on Jul 11 2018 at 19:09:03
+PLUMED: Please cite this paper when using PLUMED [1]
+PLUMED: For further information see the PLUMED web page at http://www.plumed.org
+PLUMED: Root: /Users/gareth/MD_code/lammps-permanent/lammps/lib/plumed/plumed2-2.4.2/
+PLUMED: For installed feature, see /Users/gareth/MD_code/lammps-permanent/lammps/lib/plumed/plumed2-2.4.2//src/config/config.txt
+PLUMED: Molecular dynamics engine: LAMMPS
+PLUMED: Precision of reals: 8
+PLUMED: Running over 1 node
+PLUMED: Number of threads: 1
+PLUMED: Cache line size: 512
+PLUMED: Number of atoms: 2004
+PLUMED: File suffix: 
+PLUMED: FILE: plumed.dat
+PLUMED: Action UNITS
+PLUMED:   with label @0
+PLUMED:   length: A
+PLUMED:   energy: kcal/mol
+PLUMED:   time: ps
+PLUMED:   charge: e
+PLUMED:   mass: amu
+PLUMED:   using physical units
+PLUMED:   inside PLUMED, Boltzmann constant is 0.001987
+PLUMED: Action DISTANCE
+PLUMED:   with label dd
+PLUMED:   between atoms 45 48
+PLUMED:   using periodic boundary conditions
+PLUMED: Action RESTRAINT
+PLUMED:   with label @2
+PLUMED:   with arguments dd
+PLUMED:   added component to this action:  @2.bias 
+PLUMED:   at 6.000000
+PLUMED:   with harmonic force constant 2000.000000
+PLUMED:   and linear force constant 0.000000
+PLUMED:   added component to this action:  @2.force2 
+PLUMED: Action PRINT
+PLUMED:   with label @3
+PLUMED:   with stride 1
+PLUMED:   with arguments dd
+PLUMED:   on file colvar
+PLUMED:   with format  %f
+PLUMED: END FILE: plumed.dat
+PLUMED: Timestep: 0.002000
+PLUMED: KbT has not been set by the MD engine
+PLUMED: It should be set by hand where needed
+PLUMED: Relevant bibliography:
+PLUMED:   [1] Tribello, Bonomi, Branduardi, Camilloni, and Bussi, Comput. Phys. Commun. 185, 604 (2014)
+PLUMED: Please read and cite where appropriate!
+PLUMED: Finished setup
+PLUMED:                                               Cycles        Total      Average      Minumum      Maximum
+PLUMED:                                                    1     0.020354     0.020354     0.020354     0.020354
+PLUMED: 1 Prepare dependencies                           102     0.000256     0.000003     0.000001     0.000006
+PLUMED: 2 Sharing data                                   102     0.010002     0.000098     0.000078     0.000546
+PLUMED: 3 Waiting for data                               102     0.001398     0.000014     0.000011     0.000072
+PLUMED: 4 Calculating (forward loop)                     102     0.001797     0.000018     0.000013     0.000058
+PLUMED: 5 Applying (backward loop)                       102     0.002666     0.000026     0.000022     0.000062
+PLUMED: 6 Update                                         102     0.001126     0.000011     0.000007     0.000055