From ddea477068eb2111543e5bd53d1ce00e12275ec1 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Wed, 6 Sep 2023 13:47:57 -0400 Subject: [PATCH] Add test for Colvars state being read from LAMMPS binary restart file --- .../AutoDiff/test.colvars.out | 132 +++++++++++++++++ .../AutoDiff/test.colvars.state.stripped | 20 +++ .../AutoDiff/test.colvars.traj | 22 +++ .../AutoDiff/test.restart.colvars.out | 136 ++++++++++++++++++ .../test.restart.colvars.state.stripped | 20 +++ .../AutoDiff/test.restart.colvars.traj | 22 +++ .../003_binary_restart/lammps-version.txt | 1 + .../interface/003_binary_restart/notes.txt | 1 + .../interface/003_binary_restart/test.in | 34 +++++ .../interface/003_binary_restart/test.lmp.in | 23 +++ .../003_binary_restart/test.restart.lmp.in | 22 +++ 11 files changed, 433 insertions(+) create mode 100644 lammps/tests/interface/003_binary_restart/AutoDiff/test.colvars.out create mode 100644 lammps/tests/interface/003_binary_restart/AutoDiff/test.colvars.state.stripped create mode 100644 lammps/tests/interface/003_binary_restart/AutoDiff/test.colvars.traj create mode 100644 lammps/tests/interface/003_binary_restart/AutoDiff/test.restart.colvars.out create mode 100644 lammps/tests/interface/003_binary_restart/AutoDiff/test.restart.colvars.state.stripped create mode 100644 lammps/tests/interface/003_binary_restart/AutoDiff/test.restart.colvars.traj create mode 100644 lammps/tests/interface/003_binary_restart/lammps-version.txt create mode 100644 lammps/tests/interface/003_binary_restart/notes.txt create mode 100644 lammps/tests/interface/003_binary_restart/test.in create mode 100644 lammps/tests/interface/003_binary_restart/test.lmp.in create mode 100644 lammps/tests/interface/003_binary_restart/test.restart.lmp.in diff --git a/lammps/tests/interface/003_binary_restart/AutoDiff/test.colvars.out b/lammps/tests/interface/003_binary_restart/AutoDiff/test.colvars.out new file mode 100644 index 000000000..c818f9fcf --- /dev/null +++ b/lammps/tests/interface/003_binary_restart/AutoDiff/test.colvars.out @@ -0,0 +1,132 @@ +colvars: Creating proxy instance +colvars: ---------------------------------------------------------------------- +colvars: Please cite Fiorin et al, Mol Phys 2013: +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. +colvars: This version was built with the C++11 standard or higher. +colvars: Using LAMMPS interface, version "2019-08-17". +colvars: ---------------------------------------------------------------------- +colvars: Reading new configuration from file "test.in": +colvars: # indexFile = "index.ndx" +colvars: The following index groups were read from the index file "index.ndx": +colvars: Protein (104 atoms). +colvars: Protein_noH (51 atoms). +colvars: Protein_Backbone (40 atoms). +colvars: Protein_C-alpha (10 atoms). +colvars: RMSD_atoms (10 atoms). +colvars: Protein_C-alpha_1_2 (2 atoms). +colvars: Protein_C-alpha_9_10 (2 atoms). +colvars: Protein_C-alpha_1 (1 atoms). +colvars: group1 (4 atoms). +colvars: Protein_C-alpha_2 (1 atoms). +colvars: group2 (4 atoms). +colvars: Protein_C-alpha_3 (1 atoms). +colvars: group3 (4 atoms). +colvars: Protein_C-alpha_4 (1 atoms). +colvars: group4 (4 atoms). +colvars: Protein_C-alpha_5 (1 atoms). +colvars: group5 (4 atoms). +colvars: Protein_C-alpha_6 (1 atoms). +colvars: group6 (4 atoms). +colvars: Protein_C-alpha_7 (1 atoms). +colvars: group7 (4 atoms). +colvars: Protein_C-alpha_8 (1 atoms). +colvars: group8 (4 atoms). +colvars: Protein_C-alpha_9 (1 atoms). +colvars: group9 (4 atoms). +colvars: Protein_C-alpha_10 (1 atoms). +colvars: group10 (4 atoms). +colvars: heavy_atoms (51 atoms). +colvars: # smp = on [default] +colvars: # colvarsTrajFrequency = 1 +colvars: # colvarsRestartFrequency = 10 +colvars: # scriptedColvarForces = off [default] +colvars: # scriptingAfterBiases = off [default] +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new collective variable. +colvars: # name = "one" +colvars: Initializing a new "distance" component. +colvars: # name = "" [default] +colvars: # componentCoeff = 1 [default] +colvars: # componentExp = 1 [default] +colvars: # period = 0 [default] +colvars: # wrapAround = 0 [default] +colvars: # forceNoPBC = off [default] +colvars: # scalable = on [default] +colvars: Initializing atom group "group1". +colvars: # name = "" [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] +colvars: # atomsOfGroup = "" [default] +colvars: # indexGroup = "group1" +colvars: # psfSegID = [default] +colvars: # atomsFile = "" [default] +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] +colvars: # enableFitGradients = on [default] +colvars: # printAtomIDs = off [default] +colvars: Atom group "group1" defined with 4 atoms requested. +colvars: Initializing atom group "group2". +colvars: # name = "" [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] +colvars: # atomsOfGroup = "" [default] +colvars: # indexGroup = "group2" +colvars: # psfSegID = [default] +colvars: # atomsFile = "" [default] +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] +colvars: # enableFitGradients = on [default] +colvars: # printAtomIDs = off [default] +colvars: Atom group "group2" defined with 4 atoms requested. +colvars: # oneSiteSystemForce = off [default] +colvars: # oneSiteTotalForce = off [default] +colvars: All components initialized. +colvars: # timeStepFactor = 1 [default] +colvars: # width = 0.5 +colvars: # lowerBoundary = 0 [default] +colvars: # upperBoundary = 0 [default] +colvars: # expandBoundaries = off [default] +colvars: # extendedLagrangian = off [default] +colvars: # outputValue = on [default] +colvars: # outputVelocity = off [default] +colvars: # outputTotalForce = off [default] +colvars: # outputAppliedForce = on +colvars: # subtractAppliedForce = off [default] +colvars: # runAve = off [default] +colvars: # corrFunc = off [default] +colvars: ---------------------------------------------------------------------- +colvars: Collective variables initialized, 1 in total. +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new "harmonic" instance. +colvars: # name = "harmonic1" [default] +colvars: # colvars = { one } +colvars: # outputEnergy = on +colvars: # timeStepFactor = 1 [default] +colvars: # writeTISamples = off [default] +colvars: # writeTIPMF = off [default] +colvars: # centers = { 0.1 } +colvars: # targetCenters = { 0.2 } +colvars: # targetNumSteps = 10 +colvars: # targetNumStages = 0 [default] +colvars: # outputAccumulatedWork = on +colvars: # outputCenters = on +colvars: # forceConstant = 0.001 +colvars: # targetForceConstant = -1 [default] +colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). +colvars: ---------------------------------------------------------------------- +colvars: Collective variables biases initialized, 1 in total. +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module (re)initialized. +colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "rest.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Writing to colvar trajectory file "test.colvars.traj". +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". +colvars: Saving collective variables state to "rest.colvars.state". +colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". +colvars: Saving collective variables state to "rest.colvars.state". +colvars: Saving collective variables state to "test.colvars.state". +colvars: Resetting the Collective Variables module. diff --git a/lammps/tests/interface/003_binary_restart/AutoDiff/test.colvars.state.stripped b/lammps/tests/interface/003_binary_restart/AutoDiff/test.colvars.state.stripped new file mode 100644 index 000000000..b8c03e3a3 --- /dev/null +++ b/lammps/tests/interface/003_binary_restart/AutoDiff/test.colvars.state.stripped @@ -0,0 +1,20 @@ +configuration { + step 20 + dt 1.000000e+00 +} + +colvar { + name one + x 3.21927610288861e+00 +} + +restraint { + configuration { + step 20 + name harmonic1 + firstStep 0 + centers 2.00000000000000e-01 + accumulatedWork -1.22156562115015e-03 + } +} + diff --git a/lammps/tests/interface/003_binary_restart/AutoDiff/test.colvars.traj b/lammps/tests/interface/003_binary_restart/AutoDiff/test.colvars.traj new file mode 100644 index 000000000..899edf07b --- /dev/null +++ b/lammps/tests/interface/003_binary_restart/AutoDiff/test.colvars.traj @@ -0,0 +1,22 @@ +# step one fa_one E_harmonic1 x0_one W_harmonic1 + 0 3.20554673729024e+00 -1.24221869491610e-02 1.92888410749882e-02 1.00000000000000e-01 0.00000000000000e+00 + 1 3.20438161758906e+00 -1.23775264703562e-02 1.91503951905462e-02 1.10000000000000e-01 -1.23775264703563e-04 + 2 3.20388055819324e+00 -1.23355222327730e-02 1.90206385944045e-02 1.20000000000000e-01 -2.47130487031292e-04 + 3 3.20405695050090e+00 -1.22962278020036e-02 1.88996522698458e-02 1.30000000000000e-01 -3.70092765051328e-04 + 4 3.20488566343521e+00 -1.22595426537408e-02 1.87870482598613e-02 1.40000000000000e-01 -4.92688191588736e-04 + 5 3.20630523013386e+00 -1.22252209205354e-02 1.86820033194872e-02 1.50000000000000e-01 -6.14940400794091e-04 + 6 3.20822193294306e+00 -1.21928877317723e-02 1.85833139049503e-02 1.60000000000000e-01 -7.36869278111813e-04 + 7 3.21051524726036e+00 -1.21620609890414e-02 1.84894659376454e-02 1.70000000000000e-01 -8.58489888002227e-04 + 8 3.21304438443477e+00 -1.21321775377391e-02 1.83987164759025e-02 1.80000000000000e-01 -9.79811663379618e-04 + 9 3.21565597399793e+00 -1.21026238959917e-02 1.83091881459787e-02 1.90000000000000e-01 -1.10083790233954e-03 + 10 3.21819297026538e+00 -1.20727718810615e-02 1.82189776115188e-02 2.00000000000000e-01 -1.22156562115015e-03 + 11 3.22050455244023e+00 -1.20820182097609e-02 1.82468955026243e-02 2.00000000000000e-01 -1.22156562115015e-03 + 12 3.22245626645718e+00 -1.20898250658287e-02 1.82704837652926e-02 2.00000000000000e-01 -1.22156562115015e-03 + 13 3.22393923848317e+00 -1.20957569539327e-02 1.82884170360763e-02 2.00000000000000e-01 -1.22156562115015e-03 + 14 3.22487721259280e+00 -1.20995088503712e-02 1.82997643025264e-02 2.00000000000000e-01 -1.22156562115015e-03 + 15 3.22523054868521e+00 -1.21009221947408e-02 1.83040397453964e-02 2.00000000000000e-01 -1.22156562115015e-03 + 16 3.22499693749777e+00 -1.20999877499911e-02 1.83012129437417e-02 2.00000000000000e-01 -1.22156562115015e-03 + 17 3.22420921060027e+00 -1.20968368424011e-02 1.82916826989590e-02 2.00000000000000e-01 -1.22156562115015e-03 + 18 3.22293098631693e+00 -1.20917239452677e-02 1.82762234960701e-02 2.00000000000000e-01 -1.22156562115015e-03 + 19 3.22125091863508e+00 -1.20850036745403e-02 1.82559142267067e-02 2.00000000000000e-01 -1.22156562115015e-03 + 20 3.21927610288861e+00 -1.20771044115544e-02 1.82320563709485e-02 2.00000000000000e-01 -1.22156562115015e-03 diff --git a/lammps/tests/interface/003_binary_restart/AutoDiff/test.restart.colvars.out b/lammps/tests/interface/003_binary_restart/AutoDiff/test.restart.colvars.out new file mode 100644 index 000000000..604ec03c8 --- /dev/null +++ b/lammps/tests/interface/003_binary_restart/AutoDiff/test.restart.colvars.out @@ -0,0 +1,136 @@ +colvars: Creating proxy instance +colvars: ---------------------------------------------------------------------- +colvars: Please cite Fiorin et al, Mol Phys 2013: +colvars: https://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. +colvars: This version was built with the C++11 standard or higher. +colvars: Using LAMMPS interface, version "2019-08-17". +colvars: ---------------------------------------------------------------------- +colvars: Reading new configuration from file "test.in": +colvars: # indexFile = "index.ndx" +colvars: The following index groups were read from the index file "index.ndx": +colvars: Protein (104 atoms). +colvars: Protein_noH (51 atoms). +colvars: Protein_Backbone (40 atoms). +colvars: Protein_C-alpha (10 atoms). +colvars: RMSD_atoms (10 atoms). +colvars: Protein_C-alpha_1_2 (2 atoms). +colvars: Protein_C-alpha_9_10 (2 atoms). +colvars: Protein_C-alpha_1 (1 atoms). +colvars: group1 (4 atoms). +colvars: Protein_C-alpha_2 (1 atoms). +colvars: group2 (4 atoms). +colvars: Protein_C-alpha_3 (1 atoms). +colvars: group3 (4 atoms). +colvars: Protein_C-alpha_4 (1 atoms). +colvars: group4 (4 atoms). +colvars: Protein_C-alpha_5 (1 atoms). +colvars: group5 (4 atoms). +colvars: Protein_C-alpha_6 (1 atoms). +colvars: group6 (4 atoms). +colvars: Protein_C-alpha_7 (1 atoms). +colvars: group7 (4 atoms). +colvars: Protein_C-alpha_8 (1 atoms). +colvars: group8 (4 atoms). +colvars: Protein_C-alpha_9 (1 atoms). +colvars: group9 (4 atoms). +colvars: Protein_C-alpha_10 (1 atoms). +colvars: group10 (4 atoms). +colvars: heavy_atoms (51 atoms). +colvars: # smp = on [default] +colvars: # colvarsTrajFrequency = 1 +colvars: # colvarsRestartFrequency = 10 +colvars: # scriptedColvarForces = off [default] +colvars: # scriptingAfterBiases = off [default] +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new collective variable. +colvars: # name = "one" +colvars: Initializing a new "distance" component. +colvars: # name = "" [default] +colvars: # componentCoeff = 1 [default] +colvars: # componentExp = 1 [default] +colvars: # period = 0 [default] +colvars: # wrapAround = 0 [default] +colvars: # forceNoPBC = off [default] +colvars: # scalable = on [default] +colvars: Initializing atom group "group1". +colvars: # name = "" [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] +colvars: # atomsOfGroup = "" [default] +colvars: # indexGroup = "group1" +colvars: # psfSegID = [default] +colvars: # atomsFile = "" [default] +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] +colvars: # enableFitGradients = on [default] +colvars: # printAtomIDs = off [default] +colvars: Atom group "group1" defined with 4 atoms requested. +colvars: Initializing atom group "group2". +colvars: # name = "" [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] +colvars: # atomsOfGroup = "" [default] +colvars: # indexGroup = "group2" +colvars: # psfSegID = [default] +colvars: # atomsFile = "" [default] +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] +colvars: # enableFitGradients = on [default] +colvars: # printAtomIDs = off [default] +colvars: Atom group "group2" defined with 4 atoms requested. +colvars: # oneSiteSystemForce = off [default] +colvars: # oneSiteTotalForce = off [default] +colvars: All components initialized. +colvars: # timeStepFactor = 1 [default] +colvars: # width = 0.5 +colvars: # lowerBoundary = 0 [default] +colvars: # upperBoundary = 0 [default] +colvars: # expandBoundaries = off [default] +colvars: # extendedLagrangian = off [default] +colvars: # outputValue = on [default] +colvars: # outputVelocity = off [default] +colvars: # outputTotalForce = off [default] +colvars: # outputAppliedForce = on +colvars: # subtractAppliedForce = off [default] +colvars: # runAve = off [default] +colvars: # corrFunc = off [default] +colvars: ---------------------------------------------------------------------- +colvars: Collective variables initialized, 1 in total. +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new "harmonic" instance. +colvars: # name = "harmonic1" [default] +colvars: # colvars = { one } +colvars: # outputEnergy = on +colvars: # timeStepFactor = 1 [default] +colvars: # writeTISamples = off [default] +colvars: # writeTIPMF = off [default] +colvars: # centers = { 0.1 } +colvars: # targetCenters = { 0.2 } +colvars: # targetNumSteps = 10 +colvars: # targetNumStages = 0 [default] +colvars: # outputAccumulatedWork = on +colvars: # outputCenters = on +colvars: # forceConstant = 0.001 +colvars: # targetForceConstant = -1 [default] +colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). +colvars: ---------------------------------------------------------------------- +colvars: Collective variables biases initialized, 1 in total. +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module (re)initialized. +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Restarting from file "test.colvars.state". +colvars: Restarting collective variable "one" from value: 3.21928 +colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "rest.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Writing to colvar trajectory file "test.restart.colvars.traj". +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". +colvars: Saving collective variables state to "rest.colvars.state". +colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". +colvars: Saving collective variables state to "rest.colvars.state". +colvars: Saving collective variables state to "test.restart.colvars.state". +colvars: Resetting the Collective Variables module. diff --git a/lammps/tests/interface/003_binary_restart/AutoDiff/test.restart.colvars.state.stripped b/lammps/tests/interface/003_binary_restart/AutoDiff/test.restart.colvars.state.stripped new file mode 100644 index 000000000..897c1b1ee --- /dev/null +++ b/lammps/tests/interface/003_binary_restart/AutoDiff/test.restart.colvars.state.stripped @@ -0,0 +1,20 @@ +configuration { + step 40 + dt 1.000000e+00 +} + +colvar { + name one + x 3.21816782210277e+00 +} + +restraint { + configuration { + step 40 + name harmonic1 + firstStep 0 + centers 2.00000000000000e-01 + accumulatedWork -1.22156562115015e-03 + } +} + diff --git a/lammps/tests/interface/003_binary_restart/AutoDiff/test.restart.colvars.traj b/lammps/tests/interface/003_binary_restart/AutoDiff/test.restart.colvars.traj new file mode 100644 index 000000000..d7668f2c5 --- /dev/null +++ b/lammps/tests/interface/003_binary_restart/AutoDiff/test.restart.colvars.traj @@ -0,0 +1,22 @@ +# step one fa_one E_harmonic1 x0_one W_harmonic1 + 20 3.21927610420273e+00 -1.20771044168109e-02 1.82320563868192e-02 2.00000000000000e-01 -1.22156562115015e-03 + 21 3.21712493217758e+00 -1.20684997287103e-02 1.82060857127351e-02 2.00000000000000e-01 -1.22156562115015e-03 + 22 3.21491957781060e+00 -1.20596783112424e-02 1.81794801213313e-02 2.00000000000000e-01 -1.22156562115015e-03 + 23 3.21277838638075e+00 -1.20511135455230e-02 1.81536672108860e-02 2.00000000000000e-01 -1.22156562115015e-03 + 24 3.21080868797887e+00 -1.20432347519155e-02 1.81299379112181e-02 2.00000000000000e-01 -1.22156562115015e-03 + 25 3.20910075273950e+00 -1.20364030109580e-02 1.81093746802748e-02 2.00000000000000e-01 -1.22156562115015e-03 + 26 3.20772353744991e+00 -1.20308941497996e-02 1.80928017554604e-02 2.00000000000000e-01 -1.22156562115015e-03 + 27 3.20672256044185e+00 -1.20268902417674e-02 1.80807611109400e-02 2.00000000000000e-01 -1.22156562115015e-03 + 28 3.20611979984341e+00 -1.20244791993736e-02 1.80735125020211e-02 2.00000000000000e-01 -1.22156562115015e-03 + 29 3.20591518168161e+00 -1.20236607267264e-02 1.80710521589280e-02 2.00000000000000e-01 -1.22156562115015e-03 + 30 3.20608917462516e+00 -1.20243566985006e-02 1.80731442515971e-02 2.00000000000000e-01 -1.22156562115015e-03 + 31 3.20660613772624e+00 -1.20264245509050e-02 1.80793609348262e-02 2.00000000000000e-01 -1.22156562115015e-03 + 32 3.20741824461812e+00 -1.20296729784725e-02 1.80891289961239e-02 2.00000000000000e-01 -1.22156562115015e-03 + 33 3.20846986624845e+00 -1.20338794649938e-02 1.81017818722499e-02 2.00000000000000e-01 -1.22156562115015e-03 + 34 3.20970218001743e+00 -1.20388087200697e-02 1.81166144248033e-02 2.00000000000000e-01 -1.22156562115015e-03 + 35 3.21105763094978e+00 -1.20442305237991e-02 1.81329361138018e-02 2.00000000000000e-01 -1.22156562115015e-03 + 36 3.21248380017773e+00 -1.20499352007109e-02 1.81501172926665e-02 2.00000000000000e-01 -1.22156562115015e-03 + 37 3.21393637834814e+00 -1.20557455133925e-02 1.81676249854606e-02 2.00000000000000e-01 -1.22156562115015e-03 + 38 3.21538117931034e+00 -1.20615247172414e-02 1.81850473130780e-02 2.00000000000000e-01 -1.22156562115015e-03 + 39 3.21679532830021e+00 -1.20671813132008e-02 1.82021081057079e-02 2.00000000000000e-01 -1.22156562115015e-03 + 40 3.21816782210277e+00 -1.20726712884111e-02 1.82186740047531e-02 2.00000000000000e-01 -1.22156562115015e-03 diff --git a/lammps/tests/interface/003_binary_restart/lammps-version.txt b/lammps/tests/interface/003_binary_restart/lammps-version.txt new file mode 100644 index 000000000..646d758cf --- /dev/null +++ b/lammps/tests/interface/003_binary_restart/lammps-version.txt @@ -0,0 +1 @@ +LAMMPS (12 Dec 2018) diff --git a/lammps/tests/interface/003_binary_restart/notes.txt b/lammps/tests/interface/003_binary_restart/notes.txt new file mode 100644 index 000000000..ee0c0596f --- /dev/null +++ b/lammps/tests/interface/003_binary_restart/notes.txt @@ -0,0 +1 @@ +Based on 000_distance_harmonic-centers-moving diff --git a/lammps/tests/interface/003_binary_restart/test.in b/lammps/tests/interface/003_binary_restart/test.in new file mode 100644 index 000000000..165428a9d --- /dev/null +++ b/lammps/tests/interface/003_binary_restart/test.in @@ -0,0 +1,34 @@ +colvarsTrajFrequency 1 +colvarsRestartFrequency 10 +indexFile index.ndx + +colvar { + + name one + + outputAppliedForce on + + width 0.5 + + distance { + group1 { + indexGroup group1 + } + group2 { + indexGroup group2 + } + } +} + +harmonic { + colvars one + centers 0.1 + forceConstant 0.001 + + targetCenters 0.2 + targetNumSteps 10 + + outputEnergy yes + outputCenters yes + outputAccumulatedWork yes +} diff --git a/lammps/tests/interface/003_binary_restart/test.lmp.in b/lammps/tests/interface/003_binary_restart/test.lmp.in new file mode 100644 index 000000000..042dbc48e --- /dev/null +++ b/lammps/tests/interface/003_binary_restart/test.lmp.in @@ -0,0 +1,23 @@ +# -*- lammps -*- + +shell ln -fs "../common/da.ndx" "index.ndx" +shell ln -fs "../common/da-Calpha.xyz" "rmsd_atoms_refpos.xyz" +shell ln -fs "../common/da-Calpha-310turn.xyz" "rmsd_atoms_refpos2.xyz" +shell ln -fs "../common/da-noh.xyz" "heavy_atoms_refpos.xyz" +shell ln -fs "../common/da-Calpha-random.xyz" "rmsd_atoms_random.xyz" + +include ../common/charmmff.lmp.in + +# Contains positions and velocities from da.coor.pdb and da.vel.pdb +read_data ../common/da.lmp.data + +include ../common/fixes.lmp.in + +log test.out + +fix Colvars all colvars ${colvars_config} output test + +include ../common/md.lmp.in + +write_data test.lmp.data +write_restart test.lmp.bin diff --git a/lammps/tests/interface/003_binary_restart/test.restart.lmp.in b/lammps/tests/interface/003_binary_restart/test.restart.lmp.in new file mode 100644 index 000000000..fed0a1a74 --- /dev/null +++ b/lammps/tests/interface/003_binary_restart/test.restart.lmp.in @@ -0,0 +1,22 @@ +# -*- lammps -*- + +include ../common/charmmff.lmp.in + +read_restart test.lmp.bin + +include ../common/fixes.lmp.in + +log test.restart.out + +fix Colvars all colvars ${colvars_config} output test.restart + +include ../common/md.lmp.in + +write_data test.restart.lmp.data +write_restart test.restart.lmp.bin + +shell rm -f "index.ndx" +shell rm -f "rmsd_atoms_refpos.xyz" +shell rm -f "heavy_atoms_refpos.xyz" +shell rm -f "rmsd_atoms_refpos2.xyz" +shell rm -f "rmsd_atoms_random.xyz"