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Merge remote branch 'lammps-ro/master' into lammps-icms

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Resolved Conflicts:
	src/atom.cpp
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Axel Kohlmeyer
2014-04-08 12:56:10 +02:00
parent 87e1bc1821 2292ba2c67
commit fb3a956155
15 changed files with 1120 additions and 33 deletions
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2
doc/Eqs/pair_tersoff_zbl.tex
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@ -24,7 +24,7 @@ f_F(r_{ij}) & = & \frac{1}{1 + e^{-A_F(r_{ij} - r_C)}}\\
f_A(r) & = & -B \exp (-\lambda_2 r) \\
b_{ij} & = & \left( 1 + \beta^n {\zeta_{ij}}^n \right)^{-\frac{1}{2n}} \\
\zeta_{ij} & = & \sum_{k \neq i,j} f_C(r_{ik}) g(\theta_{ijk})
\exp \left[ {\lambda_3}^3 (r_{ij} - r_{ik})^m \right] \\
\exp \left[ {\lambda_3}^m (r_{ij} - r_{ik})^m \right] \\
g(\theta) & = & \gamma_{ijk} \left( 1 + \frac{c^2}{d^2} -
\frac{c^2}{\left[ d^2 +
(\cos \theta - \cos \theta_0)^2\right]} \right)

14
doc/fix_property_atom.html
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@ -87,18 +87,18 @@ seamlessly integrated with the rest of the code.
</P>
<P>The new atom properties encode values that migrate with atoms to new
processors and are written to restart files. If you want the new
properties to also be defined for ghost atoms, then use the <I>border</I>
properties to also be defined for ghost atoms, then use the <I>ghost</I>
keyword with a value of <I>yes</I>. This will invoke extra communication
when ghost atoms are created (at every re-neighboring) to insure the
new properties are also defined for the ghost atoms.
new properties are also defined for the ghost atoms.
</P>
<P>IMPORTANT NOTE: The properties for ghost atoms are not updated every
timestep, but only once every few steps when neighbor lists are
re-built. Thus the <I>border</I> keyword is suitable for static
properties, like molecule IDs, but not for dynamic properties that
change every step. In that case, the code you add to LAMMPS to change
the properties will also need to communicate their new values, an
operation that can be invoked from within a <A HREF = "pair_style.html">pair
re-built. Thus the <I>ghost</I> keyword is suitable for static properties,
like molecule IDs, but not for dynamic properties that change every
step. For the latter, the code you add to LAMMPS to change the
properties will also need to communicate their new values to/from
ghost atoms, an operation that can be invoked from within a <A HREF = "pair_style.html">pair
style</A> or <A HREF = "fix.html">fix</A> or <A HREF = "compute.html">compute</A>
that you write.
</P>

14
doc/fix_property_atom.txt
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@ -77,18 +77,18 @@ seamlessly integrated with the rest of the code.
The new atom properties encode values that migrate with atoms to new
processors and are written to restart files. If you want the new
properties to also be defined for ghost atoms, then use the {border}
properties to also be defined for ghost atoms, then use the {ghost}
keyword with a value of {yes}. This will invoke extra communication
when ghost atoms are created (at every re-neighboring) to insure the
new properties are also defined for the ghost atoms.
new properties are also defined for the ghost atoms.
IMPORTANT NOTE: The properties for ghost atoms are not updated every
timestep, but only once every few steps when neighbor lists are
re-built. Thus the {border} keyword is suitable for static
properties, like molecule IDs, but not for dynamic properties that
change every step. In that case, the code you add to LAMMPS to change
the properties will also need to communicate their new values, an
operation that can be invoked from within a "pair
re-built. Thus the {ghost} keyword is suitable for static properties,
like molecule IDs, but not for dynamic properties that change every
step. For the latter, the code you add to LAMMPS to change the
properties will also need to communicate their new values to/from
ghost atoms, an operation that can be invoked from within a "pair
style"_pair_style.html or "fix"_fix.html or "compute"_compute.html
that you write.

19
doc/pair_tersoff_zbl.html
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@ -136,14 +136,20 @@ three-body parameters for SiCSi and SiSiC entries will not, in
general, be the same. The parameters used for the two-body
interaction come from the entry where the 2nd element is repeated.
Thus the two-body parameters for Si interacting with C, comes from the
SiCC entry. By symmetry, the twobody parameters in the SiCC and CSiSi
entries should thus be the same. The parameters used for a particular
SiCC entry.
</P>
<P>The parameters used for a particular
three-body interaction come from the entry with the corresponding
three elements. The parameters used only for two-body interactions
(n, beta, lambda2, B, lambda1, and A) in entries whose 2nd and 3rd
element are different (e.g. SiCSi) are not used for anything and can
be set to 0.0 if desired.
</P>
<P>Note that the twobody parameters in entries such as SiCC and CSiSi
are often the same, due to the common use of symmetric mixing rules,
but this is not always the case. For example, the beta and n parameters in
Tersoff_2 <A HREF = "#Tersoff_2">(Tersoff_2)</A> are not symmetric.
</P>
<P>We chose the above form so as to enable users to define all commonly
used variants of the Tersoff portion of the potential. In particular,
our form reduces to the original Tersoff form when m = 3 and gamma =
@ -154,14 +160,13 @@ different but equivalent form for alloys, which we will refer to as
Tersoff_2 potential <A HREF = "#Tersoff_2">(Tersoff_2)</A>.
</P>
<P>LAMMPS parameter values for Tersoff_2 can be obtained as follows:
gamma = 1, just as for Tersoff_1, but now lambda3 = 0 and the value of
gamma = omega_ijk, lambda3 = 0 and the value of
m has no effect. The parameters for species i and j can be calculated
using the Tersoff_2 mixing rules:
</P>
<CENTER><IMG SRC = "Eqs/pair_tersoff_2.jpg">
</CENTER>
<P>Values not shown are determined by the first atom type. Finally, the
Tersoff_2 parameters R and S must be converted to the LAMMPS
<P>Tersoff_2 parameters R and S must be converted to the LAMMPS
parameters R and D (R is different in both forms), using the following
relations: R=(R'+S')/2 and D=(S'-R')/2, where the primes indicate the
Tersoff_2 parameters.
@ -260,11 +265,11 @@ of Ions in Matter' Vol 1, 1985, Pergamon Press.
</P>
<A NAME = "Albe"></A>
<P><B>(Albe)</B> J. Nord, K. Albe, P. Erhartand K. Nordlund, J. Phys.:
<P><B>(Albe)</B> J. Nord, K. Albe, P. Erhart and K. Nordlund, J. Phys.:
Condens. Matter, 15, 5649(2003).
</P>
<A NAME = "Tersoff_2"></A>
<P><B>(Tersoff_2)</B> J. Tersoff, Phys Rev B, 39, 5566 (1989)
<P><B>(Tersoff_2)</B> J. Tersoff, Phys Rev B, 39, 5566 (1989); errata (PRB 41, 3248)
</P>
</HTML>

17
doc/pair_tersoff_zbl.txt
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@ -132,14 +132,20 @@ three-body parameters for SiCSi and SiSiC entries will not, in
general, be the same. The parameters used for the two-body
interaction come from the entry where the 2nd element is repeated.
Thus the two-body parameters for Si interacting with C, comes from the
SiCC entry. By symmetry, the twobody parameters in the SiCC and CSiSi
entries should thus be the same. The parameters used for a particular
SiCC entry.
The parameters used for a particular
three-body interaction come from the entry with the corresponding
three elements. The parameters used only for two-body interactions
(n, beta, lambda2, B, lambda1, and A) in entries whose 2nd and 3rd
element are different (e.g. SiCSi) are not used for anything and can
be set to 0.0 if desired.
Note that the twobody parameters in entries such as SiCC and CSiSi
are often the same, due to the common use of symmetric mixing rules,
but this is not always the case. For example, the beta and n parameters in
Tersoff_2 "(Tersoff_2)"_#Tersoff_2 are not symmetric.
We chose the above form so as to enable users to define all commonly
used variants of the Tersoff portion of the potential. In particular,
our form reduces to the original Tersoff form when m = 3 and gamma =
@ -150,13 +156,12 @@ different but equivalent form for alloys, which we will refer to as
Tersoff_2 potential "(Tersoff_2)"_#Tersoff_2.
LAMMPS parameter values for Tersoff_2 can be obtained as follows:
gamma = 1, just as for Tersoff_1, but now lambda3 = 0 and the value of
gamma = omega_ijk, lambda3 = 0 and the value of
m has no effect. The parameters for species i and j can be calculated
using the Tersoff_2 mixing rules:
:c,image(Eqs/pair_tersoff_2.jpg)
Values not shown are determined by the first atom type. Finally, the
Tersoff_2 parameters R and S must be converted to the LAMMPS
parameters R and D (R is different in both forms), using the following
relations: R=(R'+S')/2 and D=(S'-R')/2, where the primes indicate the
@ -253,8 +258,8 @@ units.
of Ions in Matter' Vol 1, 1985, Pergamon Press.
:link(Albe)
[(Albe)] J. Nord, K. Albe, P. Erhartand K. Nordlund, J. Phys.:
[(Albe)] J. Nord, K. Albe, P. Erhart and K. Nordlund, J. Phys.:
Condens. Matter, 15, 5649(2003).
:link(Tersoff_2)
[(Tersoff_2)] J. Tersoff, Phys Rev B, 39, 5566 (1989)
[(Tersoff_2)] J. Tersoff, Phys Rev B, 39, 5566 (1989); errata (PRB 41, 3248)

5
doc/read_restart.html
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@ -168,6 +168,11 @@ file is read.
to the restart file as broken bonds with a type of 0. Thus these
bonds will still be broken when the restart file is read.
</P>
<P>Bonds that have been broken by the <A HREF = "fix_bond_break.html">fix
bond/break</A> command have disappeared from the
system. No information about these bonds is written to the restart
file.
</P>
<P>IMPORTANT NOTE: No other information is stored in the restart file.
This means that an input script that reads a restart file should
specify settings for quantities like <A HREF = "timestep.html">timestep size</A>,

5
doc/read_restart.txt
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@ -165,6 +165,11 @@ Bonds that are broken (e.g. by a bond-breaking potential) are written
to the restart file as broken bonds with a type of 0. Thus these
bonds will still be broken when the restart file is read.
Bonds that have been broken by the "fix
bond/break"_fix_bond_break.html command have disappeared from the
system. No information about these bonds is written to the restart
file.
IMPORTANT NOTE: No other information is stored in the restart file.
This means that an input script that reads a restart file should
specify settings for quantities like "timestep size"_timestep.html,

547
examples/USER/colvars/log.peptide-colvars Normal file
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@ -0,0 +1,547 @@
LAMMPS (20 Mar 2014-ICMS)
WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100)
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
1 by 1 by 2 MPI processor grid
reading atoms ...
2004 atoms
reading velocities ...
2004 velocities
scanning bonds ...
3 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
14 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
reading bonds ...
1365 bonds
reading angles ...
786 angles
reading dihedrals ...
207 dihedrals
reading impropers ...
12 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
group peptide type <= 12
84 atoms in group peptide
group one id 2 4 5 6
4 atoms in group one
group two id 80 82 83 84
4 atoms in group two
group ref id 37
1 atoms in group ref
group colvar union one two ref
9 atoms in group colvar
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
shell "rm -f out*.colvars.*"
fix 2 all colvars peptide.colvars
fix 2a ref setforce 0.0 0.0 0.0
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
19 = # of size 2 clusters
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
#dump_modify 1 sort id
thermo_style custom step temp etotal pe ke epair ebond f_2
thermo 10
run 100
PPPM initialization ...
G vector (1/distance) = 0.268725
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0228209
estimated relative force accuracy = 6.87243e-05
using double precision FFTs
3d grid and FFT values/proc = 6776 1800
colvars: Creating proxy instance
colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2013-10-22.
colvars: # indexFile = "" [default]
colvars: # analysis = off [default]
colvars: # colvarsTrajFrequency = 1
colvars: # colvarsRestartFrequency = 1000
colvars: # colvarsTrajAppend = off [default]
colvars: The restart output state file will be "rest.colvars.state".
colvars: The final output state file will be "out.colvars.state".
colvars: Writing to colvar trajectory file "out.colvars.traj".
colvars: ----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = one
colvars: Initializing a new "distance" component.
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # period = 0 [default]
colvars: # wrapAround = 0 [default]
colvars: # forceNoPBC = off [default]
colvars: # oneSiteSystemForce = off [default]
colvars: Initializing atom group "group1".
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # disableForces = off [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # enableFitGradients = on [default]
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 0.
colvars: Initializing atom group "group2".
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # disableForces = off [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # enableFitGradients = on [default]
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 0.
colvars: All components initialized.
colvars: # width = 1 [default]
colvars: # lowerBoundary = 0 [default]
colvars: # lowerWallConstant = 0 [default]
colvars: # upperBoundary = 0 [default]
colvars: # upperWallConstant = 0 [default]
colvars: # expandBoundaries = off [default]
colvars: # extendedLagrangian = off [default]
colvars: # outputValue = on [default]
colvars: # outputVelocity = off [default]
colvars: # outputSystemForce = off [default]
colvars: # outputAppliedForce = off [default]
colvars: ----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = two
colvars: Initializing a new "distance" component.
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # period = 0 [default]
colvars: # wrapAround = 0 [default]
colvars: # forceNoPBC = off [default]
colvars: # oneSiteSystemForce = off [default]
colvars: Initializing atom group "group1".
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # disableForces = off [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # enableFitGradients = on [default]
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 0.
colvars: Initializing atom group "group2".
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # disableForces = off [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # enableFitGradients = on [default]
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 0.
colvars: All components initialized.
colvars: # width = 1 [default]
colvars: # lowerBoundary = 0 [default]
colvars: # lowerWallConstant = 0 [default]
colvars: # upperBoundary = 0 [default]
colvars: # upperWallConstant = 0 [default]
colvars: # expandBoundaries = off [default]
colvars: # extendedLagrangian = off [default]
colvars: # outputValue = on [default]
colvars: # outputVelocity = off [default]
colvars: # outputSystemForce = off [default]
colvars: # outputAppliedForce = off [default]
colvars: ----------------------------------------------------------------------
colvars: Collective variables initialized, 2 in total.
colvars: ----------------------------------------------------------------------
colvars: Initializing a new "harmonic" instance.
colvars: # name = h_pot
colvars: # colvars = { one, two }
colvars: # outputEnergy = off [default]
colvars: # forceConstant = 100
colvars: # centers = { 10, 10 }
colvars: # targetCenters = { 10, 10 } [default]
colvars: # targetForceConstant = 0 [default]
colvars: # outputCenters = off [default]
colvars: # outputAccumulatedWork = off [default]
colvars: ----------------------------------------------------------------------
colvars: Collective variables biases initialized, 1 in total.
colvars: ----------------------------------------------------------------------
colvars: Collective variables module initialized.
colvars: ----------------------------------------------------------------------
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
SHAKE stats (type/ave/delta) on step 0
4 1.111 1.44264e-05
6 0.996998 7.26967e-06
8 1.08 1.32536e-05
10 1.111 1.22749e-05
12 1.08 1.11767e-05
14 0.96 0
18 0.957206 4.37979e-05
31 104.519 0.00396029
Memory usage per processor = 10.4104 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond 2
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
10 305.06198 -5058.89 -6286.1848 1227.2948 -6413.0968 58.849896 103.38344
20 311.00591 -4999.0544 -6250.2623 1251.2079 -6417.0983 47.695275 36.699706
30 314.22398 -4993.6951 -6257.8496 1264.1545 -6421.9641 35.344161 10.563914
40 297.87525 -5020.8339 -6219.2158 1198.3819 -6389.8501 27.7232 3.8354396
50 304.02085 -5056.2539 -6279.3602 1223.1063 -6456.818 55.459511 0.20679816
60 285.92595 -5104.0436 -6254.3523 1150.3087 -6435.5793 32.767289 0.69356527
70 277.83498 -5163.9751 -6281.733 1117.7579 -6447.7013 39.62715 11.433633
80 267.51476 -5206.4041 -6282.6428 1076.2386 -6456.6352 31.611841 6.3553235
90 278.15512 -5245.383 -6364.4288 1119.0458 -6499.8036 28.849902 0.36938817
SHAKE stats (type/ave/delta) on step 100
4 1.11098 8.97185e-05
6 0.996996 1.00569e-05
8 1.08 6.02346e-06
10 1.111 1.84257e-05
12 1.08 7.27136e-06
14 0.959996 0
18 0.957198 3.36078e-05
31 104.52 0.00306008
100 260.10505 -5292.689 -6339.1177 1046.4286 -6471.6693 25.361881 0.21986866
Loop time of 1.04673 on 2 procs for 100 steps with 2004 atoms
99.3% CPU use with 2 MPI tasks x 1 OpenMP threads
Performance: 16.509 ns/day 1.454 hours/ns 95.536 timesteps/s
MPI task timings breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.76537 | 0.76832 | 0.77127 | 0.3 | 73.40
Bond | 0.0024452 | 0.0025067 | 0.0025682 | 0.1 | 0.24
Kspace | 0.088877 | 0.092861 | 0.096845 | 1.3 | 8.87
Neigh | 0.13657 | 0.13657 | 0.13658 | 0.0 | 13.05
Comm | 0.0172 | 0.018169 | 0.019137 | 0.7 | 1.74
Output | 0.0002296 | 0.00031686 | 0.00040412 | 0.5 | 0.03
Modify | 0.025518 | 0.025554 | 0.025591 | 0.0 | 2.44
Other | | 0.002431 | | | 0.23
Nlocal: 1002 ave 1013 max 991 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 8629.5 ave 8641 max 8618 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 354118 ave 356534 max 351703 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 708237
Ave neighs/atom = 353.412
Ave special neighs/atom = 2.34032
Neighbor list builds = 12
Dangerous builds = 2
run 100
PPPM initialization ...
G vector (1/distance) = 0.268725
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0228209
estimated relative force accuracy = 6.87243e-05
using double precision FFTs
3d grid and FFT values/proc = 6776 1800
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
SHAKE stats (type/ave/delta) on step 100
4 1.11098 8.97185e-05
6 0.996996 1.00569e-05
8 1.08 6.02346e-06
10 1.111 1.84257e-05
12 1.08 7.27136e-06
14 0.959996 0
18 0.957198 3.36078e-05
31 104.52 0.00306008
Memory usage per processor = 10.4104 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond 2
100 260.10505 -5292.689 -6339.1177 1046.4286 -6471.6693 25.361881 0.21986866
110 266.26279 -5341.2085 -6412.4103 1071.2018 -6552.7566 33.572973 1.9229795
120 262.66439 -5386.2495 -6442.9746 1056.7251 -6587.5499 29.859549 2.712489
130 252.83437 -5422.5446 -6439.7226 1017.1779 -6580.4751 25.979056 1.2031649
140 253.85101 -5452.1904 -6473.4584 1021.268 -6609.4883 26.071526 0.30586448
150 261.31821 -5490.4808 -6541.7901 1051.3093 -6646.615 16.258546 6.904992
160 255.73714 -5521.6048 -6550.4609 1028.8561 -6658.1531 19.717543 12.339834
170 253.42881 -5540.0985 -6559.668 1019.5695 -6656.6862 23.293616 10.289885
180 248.51049 -5550.3254 -6550.1079 999.78252 -6661.4178 26.200082 3.4339077
190 250.80375 -5555.2616 -6564.2702 1009.0086 -6666.1496 25.536628 3.3495235
SHAKE stats (type/ave/delta) on step 200
4 1.111 1.81287e-06
6 0.997 7.79626e-07
8 1.08 1.08933e-06
10 1.111 2.96498e-07
12 1.08 4.69169e-07
14 0.960001 0
18 0.957201 3.76617e-06
31 104.52 0.000411076
200 251.50646 -5557.4204 -6569.256 1011.8356 -6674.0889 24.805155 7.13891
Loop time of 1.00434 on 2 procs for 100 steps with 2004 atoms
99.1% CPU use with 2 MPI tasks x 1 OpenMP threads
Performance: 17.205 ns/day 1.395 hours/ns 99.568 timesteps/s
MPI task timings breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.78001 | 0.78091 | 0.78181 | 0.1 | 77.75
Bond | 0.0025158 | 0.0025688 | 0.0026219 | 0.1 | 0.26
Kspace | 0.093375 | 0.094821 | 0.096266 | 0.5 | 9.44
Neigh | 0.080238 | 0.08025 | 0.080261 | 0.0 | 7.99
Comm | 0.01671 | 0.017204 | 0.017699 | 0.4 | 1.71
Output | 0.0002296 | 0.00031531 | 0.00040102 | 0.5 | 0.03
Modify | 0.025788 | 0.025804 | 0.02582 | 0.0 | 2.57
Other | | 0.002469 | | | 0.25
Nlocal: 1002 ave 1014 max 990 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 8654 ave 8667 max 8641 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 354044 ave 355332 max 352756 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 708088
Ave neighs/atom = 353.337
Ave special neighs/atom = 2.34032
Neighbor list builds = 7
Dangerous builds = 0
fix 2 all colvars peptide.colvars input out.colvars.state output out2
colvars: Saving collective variables state to "out.colvars.state".
run 100
PPPM initialization ...
G vector (1/distance) = 0.268725
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0228209
estimated relative force accuracy = 6.87243e-05
using double precision FFTs
3d grid and FFT values/proc = 6776 1800
colvars: Creating proxy instance
colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2013-10-22.
colvars: # indexFile = "" [default]
colvars: # analysis = off [default]
colvars: # colvarsTrajFrequency = 1
colvars: # colvarsRestartFrequency = 1000
colvars: # colvarsTrajAppend = off [default]
colvars: The restart output state file will be "rest.colvars.state".
colvars: The final output state file will be "out2.colvars.state".
colvars: Writing to colvar trajectory file "out2.colvars.traj".
colvars: ----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = one
colvars: Initializing a new "distance" component.
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # period = 0 [default]
colvars: # wrapAround = 0 [default]
colvars: # forceNoPBC = off [default]
colvars: # oneSiteSystemForce = off [default]
colvars: Initializing atom group "group1".
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # disableForces = off [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # enableFitGradients = on [default]
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 0.
colvars: Initializing atom group "group2".
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # disableForces = off [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # enableFitGradients = on [default]
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 0.
colvars: All components initialized.
colvars: # width = 1 [default]
colvars: # lowerBoundary = 0 [default]
colvars: # lowerWallConstant = 0 [default]
colvars: # upperBoundary = 0 [default]
colvars: # upperWallConstant = 0 [default]
colvars: # expandBoundaries = off [default]
colvars: # extendedLagrangian = off [default]
colvars: # outputValue = on [default]
colvars: # outputVelocity = off [default]
colvars: # outputSystemForce = off [default]
colvars: # outputAppliedForce = off [default]
colvars: ----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = two
colvars: Initializing a new "distance" component.
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # period = 0 [default]
colvars: # wrapAround = 0 [default]
colvars: # forceNoPBC = off [default]
colvars: # oneSiteSystemForce = off [default]
colvars: Initializing atom group "group1".
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # disableForces = off [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # enableFitGradients = on [default]
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 0.
colvars: Initializing atom group "group2".
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # disableForces = off [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # enableFitGradients = on [default]
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 0.
colvars: All components initialized.
colvars: # width = 1 [default]
colvars: # lowerBoundary = 0 [default]
colvars: # lowerWallConstant = 0 [default]
colvars: # upperBoundary = 0 [default]
colvars: # upperWallConstant = 0 [default]
colvars: # expandBoundaries = off [default]
colvars: # extendedLagrangian = off [default]
colvars: # outputValue = on [default]
colvars: # outputVelocity = off [default]
colvars: # outputSystemForce = off [default]
colvars: # outputAppliedForce = off [default]
colvars: ----------------------------------------------------------------------
colvars: Collective variables initialized, 2 in total.
colvars: ----------------------------------------------------------------------
colvars: Initializing a new "harmonic" instance.
colvars: # name = h_pot
colvars: # colvars = { one, two }
colvars: # outputEnergy = off [default]
colvars: # forceConstant = 100
colvars: # centers = { 10, 10 }
colvars: # targetCenters = { 10, 10 } [default]
colvars: # targetForceConstant = 0 [default]
colvars: # outputCenters = off [default]
colvars: # outputAccumulatedWork = off [default]
colvars: ----------------------------------------------------------------------
colvars: Collective variables biases initialized, 1 in total.
colvars: ----------------------------------------------------------------------
colvars: Restarting from file "out.colvars.state".
colvars: Restarting collective variable "one" from value: 10.0128
colvars: Restarting collective variable "two" from value: 9.62236
colvars: Restarting harmonic bias "h_pot".
colvars: ----------------------------------------------------------------------
colvars: Collective variables module initialized.
colvars: ----------------------------------------------------------------------
colvars: Initializing step number as firstTimestep.
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
SHAKE stats (type/ave/delta) on step 200
4 1.111 1.81287e-06
6 0.997 7.79626e-07
8 1.08 1.08933e-06
10 1.111 2.96498e-07
12 1.08 4.69169e-07
14 0.960001 0
18 0.957201 3.76617e-06
31 104.52 0.000411076
Memory usage per processor = 10.4104 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond 2
200 251.50646 -5557.4204 -6569.256 1011.8356 -6674.0889 24.805155 7.13891
210 253.15173 -5538.5647 -6557.0194 1018.4547 -6672.044 37.671405 0.61299805
220 245.19832 -5522.5253 -6508.9826 986.45735 -6628.2043 36.656213 0.04862311
230 258.65093 -5495.7204 -6536.2989 1040.5785 -6658.0891 34.855426 0.22044707
240 260.80348 -5469.8527 -6519.0912 1049.2385 -6624.1806 31.576284 3.7570152
250 269.06517 -5438.3941 -6520.8701 1082.4761 -6616.3835 25.443998 8.6642401
260 266.10873 -5397.3229 -6467.905 1070.582 -6580.6583 26.873845 8.3331291
270 272.81399 -5350.8435 -6448.4015 1097.5579 -6563.7941 23.11303 10.972811
280 279.52614 -5307.9857 -6432.5473 1124.5616 -6557.7474 33.640052 8.5474491
290 286.8015 -5260.87 -6414.7011 1153.8311 -6515.4961 28.571844 5.9093384
SHAKE stats (type/ave/delta) on step 300
4 1.111 1.79747e-05
6 0.997005 1.02624e-05
8 1.08 1.84986e-05
10 1.111 9.9852e-06
12 1.08 8.8315e-06
14 0.960008 0
18 0.957203 1.84856e-05
31 104.52 0.00169095
300 291.51723 -5216.3366 -6389.1396 1172.803 -6503.1168 27.877108 2.2481775
Loop time of 1.0092 on 2 procs for 100 steps with 2004 atoms
99.1% CPU use with 2 MPI tasks x 1 OpenMP threads
Performance: 17.123 ns/day 1.402 hours/ns 99.089 timesteps/s
MPI task timings breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.77015 | 0.77511 | 0.78007 | 0.6 | 76.80
Bond | 0.0022984 | 0.0024998 | 0.0027013 | 0.4 | 0.25
Kspace | 0.088884 | 0.093076 | 0.097267 | 1.4 | 9.22
Neigh | 0.092871 | 0.092888 | 0.092905 | 0.0 | 9.20
Comm | 0.016476 | 0.017 | 0.017524 | 0.4 | 1.68
Output | 0.00022602 | 0.00031459 | 0.00040317 | 0.5 | 0.03
Modify | 0.025814 | 0.025818 | 0.025823 | 0.0 | 2.56
Other | | 0.002488 | | | 0.25
Nlocal: 1002 ave 1024 max 980 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 8717.5 ave 8755 max 8680 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 354073 ave 358151 max 349995 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 708146
Ave neighs/atom = 353.366
Ave special neighs/atom = 2.34032
Neighbor list builds = 8
Dangerous builds = 0
colvars: Saving collective variables state to "out2.colvars.state".
Please see the log.cite file for references relevant to this simulation

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LAMMPS (20 Mar 2014-ICMS)
WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100)
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
1 by 1 by 2 MPI processor grid
reading atoms ...
2004 atoms
reading velocities ...
2004 velocities
scanning bonds ...
3 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
14 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
reading bonds ...
1365 bonds
reading angles ...
786 angles
reading dihedrals ...
207 dihedrals
reading impropers ...
12 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
group peptide type <= 12
84 atoms in group peptide
group one id 2 4 5 6
4 atoms in group one
group two id 80 82 83 84
4 atoms in group two
group ref id 37
1 atoms in group ref
group colvar union one two ref
9 atoms in group colvar
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
shell "rm -f peptide2.colvars.*"
fix 2 all colvars peptide.colvars2 output peptide2
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
19 = # of size 2 clusters
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
#dump 1 colvar custom 1 dump.colvar2.lammpstrj id xu yu zu fx fy fz
#dump_modify 1 sort id
thermo_style custom step temp etotal pe ke epair ebond f_2
thermo 10
run 100
PPPM initialization ...
G vector (1/distance) = 0.268725
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0228209
estimated relative force accuracy = 6.87243e-05
using double precision FFTs
3d grid and FFT values/proc = 6776 1800
colvars: Creating proxy instance
colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2013-10-22.
colvars: # indexFile = "" [default]
colvars: # analysis = off [default]
colvars: # colvarsTrajFrequency = 1
colvars: # colvarsRestartFrequency = 1000
colvars: # colvarsTrajAppend = off [default]
colvars: The restart output state file will be "rest.colvars.state".
colvars: The final output state file will be "peptide2.colvars.state".
colvars: Writing to colvar trajectory file "peptide2.colvars.traj".
colvars: ----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = one
colvars: Initializing a new "distance" component.
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # period = 0 [default]
colvars: # wrapAround = 0 [default]
colvars: # forceNoPBC = off [default]
colvars: # oneSiteSystemForce = off [default]
colvars: Initializing atom group "group1".
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # disableForces = off [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # enableFitGradients = on [default]
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 0.
colvars: Initializing atom group "group2".
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # disableForces = off [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # enableFitGradients = on [default]
colvars: Atom group "group2" defined, 4 atoms initialized: total mass = 0.
colvars: All components initialized.
colvars: # width = 1 [default]
colvars: # lowerBoundary = 0 [default]
colvars: # lowerWallConstant = 0 [default]
colvars: # upperBoundary = 0 [default]
colvars: # upperWallConstant = 0 [default]
colvars: # expandBoundaries = off [default]
colvars: # extendedLagrangian = off [default]
colvars: # outputValue = on [default]
colvars: # outputVelocity = off [default]
colvars: # outputSystemForce = off [default]
colvars: # outputAppliedForce = off [default]
colvars: ----------------------------------------------------------------------
colvars: Collective variables initialized, 1 in total.
colvars: ----------------------------------------------------------------------
colvars: Initializing a new "harmonic" instance.
colvars: # name = h_pot
colvars: # colvars = { one }
colvars: # outputEnergy = off [default]
colvars: # forceConstant = 100
colvars: # centers = { 10 }
colvars: # targetCenters = { 10 } [default]
colvars: # targetForceConstant = 0 [default]
colvars: # outputCenters = off [default]
colvars: # outputAccumulatedWork = off [default]
colvars: ----------------------------------------------------------------------
colvars: Collective variables biases initialized, 1 in total.
colvars: ----------------------------------------------------------------------
colvars: Collective variables module initialized.
colvars: ----------------------------------------------------------------------
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 15.035.
SHAKE stats (type/ave/delta) on step 0
4 1.111 1.44264e-05
6 0.996998 7.26967e-06
8 1.08 1.32536e-05
10 1.111 1.22749e-05
12 1.08 1.11767e-05
14 0.96 0
18 0.957206 4.37979e-05
31 104.519 0.00396029
Memory usage per processor = 10.4103 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond 2
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
10 333.47973 -4982.3893 -6324.0116 1341.6223 -6400.417 21.367753 12.393269
20 309.56974 -4999.4934 -6244.9234 1245.43 -6401.6969 43.595447 13.004393
30 316.97689 -5025.5598 -6300.7895 1275.2297 -6422.5335 27.323113 6.7588862
40 297.55811 -5088.2155 -6285.3215 1197.106 -6395.3714 13.676871 25.625154
50 296.80002 -5117.2927 -6311.3488 1194.0561 -6451.8274 30.631277 5.3320302
60 281.72798 -5188.494 -6321.9138 1133.4198 -6427.8833 26.28765 20.573958
70 277.26045 -5224.8416 -6340.2881 1115.4465 -6447.8495 27.742889 0.69414895
80 268.01458 -5281.8501 -6360.0996 1078.2495 -6496.6062 20.300729 5.260642
90 270.43384 -5334.0847 -6422.0671 1087.9824 -6563.2486 39.845992 1.183249
SHAKE stats (type/ave/delta) on step 100
4 1.11096 0.000191466
6 0.996989 3.5552e-05
8 1.08 9.10001e-06
10 1.111 1.58547e-05
12 1.08 5.80613e-06
14 0.959997 0
18 0.957198 2.92454e-05
31 104.52 0.00239929
100 260.35617 -5387.2298 -6434.6687 1047.4389 -6534.1957 20.246734 0.075048991
Loop time of 1.07439 on 2 procs for 100 steps with 2004 atoms
98.2% CPU use with 2 MPI tasks x 1 OpenMP threads
Performance: 16.084 ns/day 1.492 hours/ns 93.076 timesteps/s
MPI task timings breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.77154 | 0.77308 | 0.77462 | 0.2 | 71.96
Bond | 0.0023637 | 0.0025266 | 0.0026896 | 0.3 | 0.24
Kspace | 0.095779 | 0.097411 | 0.099043 | 0.5 | 9.07
Neigh | 0.15521 | 0.15521 | 0.15522 | 0.0 | 14.45
Comm | 0.018134 | 0.018364 | 0.018594 | 0.2 | 1.71
Output | 0.00024295 | 0.00032854 | 0.00041413 | 0.5 | 0.03
Modify | 0.024936 | 0.024973 | 0.02501 | 0.0 | 2.32
Other | | 0.002498 | | | 0.23
Nlocal: 1002 ave 1010 max 994 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 8645 ave 8652 max 8638 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 354116 ave 356373 max 351860 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 708233
Ave neighs/atom = 353.41
Ave special neighs/atom = 2.34032
Neighbor list builds = 13
Dangerous builds = 1
colvars: Saving collective variables state to "peptide2.colvars.state".
Please see the log.cite file for references relevant to this simulation

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LAMMPS (20 Mar 2014-ICMS)
WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100)
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
1 by 1 by 2 MPI processor grid
reading atoms ...
2004 atoms
reading velocities ...
2004 velocities
scanning bonds ...
3 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
14 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
reading bonds ...
1365 bonds
reading angles ...
786 angles
reading dihedrals ...
207 dihedrals
reading impropers ...
12 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
group peptide type <= 12
84 atoms in group peptide
group one id 2 4 5 6
4 atoms in group one
group two id 80 82 83 84
4 atoms in group two
group ref id 37
1 atoms in group ref
group colvar union one two ref
9 atoms in group colvar
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
fix 3a one spring couple ref 100.0 0.0 0.0 0.0 10.0
fix 3b two spring couple ref 100.0 0.0 0.0 0.0 10.0
fix 2a ref setforce 0.0 0.0 0.0
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
19 = # of size 2 clusters
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
dump 1 colvar custom 1 dump.spring.lammpstrj id xu yu zu fx fy fz
dump_modify 1 sort id
variable sp equal f_3a+f_3b
thermo_style custom step temp etotal pe ke epair ebond v_sp
thermo 10
run 100
PPPM initialization ...
G vector (1/distance) = 0.268725
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0228209
estimated relative force accuracy = 6.87243e-05
using double precision FFTs
3d grid and FFT values/proc = 6776 1800
SHAKE stats (type/ave/delta) on step 0
4 1.111 1.44264e-05
6 0.996998 7.26967e-06
8 1.08 1.32536e-05
10 1.111 1.22749e-05
12 1.08 1.11767e-05
14 0.96 0
18 0.957206 4.37979e-05
31 104.519 0.00396029
Memory usage per processor = 11.5952 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond sp
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
10 305.06198 -5058.89 -6286.1848 1227.2948 -6413.0968 58.849896 103.38344
20 311.00591 -4999.0544 -6250.2623 1251.2079 -6417.0983 47.695275 36.699706
30 314.22398 -4993.6951 -6257.8496 1264.1545 -6421.9641 35.344161 10.563914
40 297.87525 -5020.8339 -6219.2158 1198.3819 -6389.8501 27.7232 3.8354396
50 304.02085 -5056.2539 -6279.3602 1223.1063 -6456.8181 55.459511 0.20679816
60 285.92595 -5104.0436 -6254.3523 1150.3087 -6435.5793 32.767289 0.69356527
70 277.83498 -5163.9751 -6281.733 1117.7579 -6447.7013 39.627151 11.433633
80 267.51476 -5206.4042 -6282.6428 1076.2386 -6456.6353 31.611841 6.3553235
90 278.15512 -5245.383 -6364.4289 1119.0458 -6499.8037 28.849902 0.36938816
SHAKE stats (type/ave/delta) on step 100
4 1.11098 8.97185e-05
6 0.996996 1.00569e-05
8 1.08 6.02346e-06
10 1.111 1.84257e-05
12 1.08 7.27136e-06
14 0.959996 0
18 0.957198 3.36078e-05
31 104.52 0.00306008
100 260.10505 -5292.689 -6339.1176 1046.4286 -6471.6693 25.361881 0.21986866
Loop time of 1.07153 on 2 procs for 100 steps with 2004 atoms
98.1% CPU use with 2 MPI tasks x 1 OpenMP threads
Performance: 16.126 ns/day 1.488 hours/ns 93.325 timesteps/s
MPI task timings breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.76688 | 0.77633 | 0.78579 | 1.1 | 72.45
Bond | 0.0024021 | 0.0025222 | 0.0026424 | 0.2 | 0.24
Kspace | 0.095468 | 0.10394 | 0.1124 | 2.6 | 9.70
Neigh | 0.13518 | 0.13518 | 0.13519 | 0.0 | 12.62
Comm | 0.018154 | 0.018954 | 0.019754 | 0.6 | 1.77
Output | 0.005975 | 0.0066451 | 0.0073152 | 0.8 | 0.62
Modify | 0.025297 | 0.025306 | 0.025314 | 0.0 | 2.36
Other | | 0.002651 | | | 0.25
Nlocal: 1002 ave 1013 max 991 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 8629.5 ave 8641 max 8618 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 354118 ave 356534 max 351703 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 708237
Ave neighs/atom = 353.412
Ave special neighs/atom = 2.34032
Neighbor list builds = 12
Dangerous builds = 2

145
examples/USER/colvars/log.peptide-spring2 Normal file
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@ -0,0 +1,145 @@
LAMMPS (20 Mar 2014-ICMS)
WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100)
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
1 by 1 by 2 MPI processor grid
reading atoms ...
2004 atoms
reading velocities ...
2004 velocities
scanning bonds ...
3 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
14 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
reading bonds ...
1365 bonds
reading angles ...
786 angles
reading dihedrals ...
207 dihedrals
reading impropers ...
12 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
group peptide type <= 12
84 atoms in group peptide
group one id 2 4 5 6
4 atoms in group one
group two id 80 82 83 84
4 atoms in group two
group ref id 37
1 atoms in group ref
group colvar union one two ref
9 atoms in group colvar
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
fix 3 one spring couple two 100.0 0.0 0.0 0.0 10.0
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
19 = # of size 2 clusters
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
dump 1 colvar custom 1 dump.spring2.lammpstrj id xu yu zu fx fy fz
dump_modify 1 sort id
thermo_style custom step temp etotal pe ke epair ebond f_3
thermo 10
run 100
PPPM initialization ...
G vector (1/distance) = 0.268725
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0228209
estimated relative force accuracy = 6.87243e-05
using double precision FFTs
3d grid and FFT values/proc = 6776 1800
SHAKE stats (type/ave/delta) on step 0
4 1.111 1.44264e-05
6 0.996998 7.26967e-06
8 1.08 1.32536e-05
10 1.111 1.22749e-05
12 1.08 1.11767e-05
14 0.96 0
18 0.957206 4.37979e-05
31 104.519 0.00396029
Memory usage per processor = 11.5952 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond 3
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
10 333.47973 -4982.3893 -6324.0116 1341.6223 -6400.417 21.367753 12.393269
20 309.56974 -4999.4934 -6244.9234 1245.43 -6401.6969 43.595447 13.004393
30 316.97689 -5025.5598 -6300.7895 1275.2297 -6422.5335 27.323113 6.7588862
40 297.55811 -5088.2155 -6285.3215 1197.106 -6395.3714 13.676871 25.625154
50 296.80002 -5117.2927 -6311.3488 1194.0561 -6451.8274 30.631277 5.3320302
60 281.72798 -5188.494 -6321.9138 1133.4198 -6427.8834 26.28765 20.573958
70 277.26045 -5224.8415 -6340.288 1115.4465 -6447.8494 27.742889 0.69414895
80 268.01458 -5281.8501 -6360.0995 1078.2495 -6496.6062 20.300729 5.260642
90 270.43384 -5334.0847 -6422.0671 1087.9824 -6563.2486 39.845992 1.183249
SHAKE stats (type/ave/delta) on step 100
4 1.11096 0.000191466
6 0.996989 3.5552e-05
8 1.08 9.10001e-06
10 1.111 1.58547e-05
12 1.08 5.80613e-06
14 0.959997 0
18 0.957198 2.92454e-05
31 104.52 0.00239929
100 260.35617 -5387.2297 -6434.6686 1047.4389 -6534.1956 20.246734 0.075048996
Loop time of 1.07264 on 2 procs for 100 steps with 2004 atoms
98.6% CPU use with 2 MPI tasks x 1 OpenMP threads
Performance: 16.110 ns/day 1.490 hours/ns 93.228 timesteps/s
MPI task timings breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.76647 | 0.77219 | 0.77792 | 0.7 | 71.99
Bond | 0.0024974 | 0.0025403 | 0.0025833 | 0.1 | 0.24
Kspace | 0.091998 | 0.096921 | 0.10184 | 1.6 | 9.04
Neigh | 0.14764 | 0.14765 | 0.14767 | 0.0 | 13.77
Comm | 0.018904 | 0.01937 | 0.019835 | 0.3 | 1.81
Output | 0.005985 | 0.0067209 | 0.0074568 | 0.9 | 0.63
Modify | 0.024529 | 0.024536 | 0.024542 | 0.0 | 2.29
Other | | 0.002705 | | | 0.25
Nlocal: 1002 ave 1010 max 994 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 8645 ave 8652 max 8638 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 354116 ave 356373 max 351860 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 708233
Ave neighs/atom = 353.41
Ave special neighs/atom = 2.34032
Neighbor list builds = 13
Dangerous builds = 1

7
src/atom.cpp
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@ -162,8 +162,7 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
tag_enable = 1;
map_style = map_user = 0;
map_tag_max = -1;
map_maxarray = 0;
map_nhash = -1;
map_maxarray = map_nhash = 0;
max_same = 0;
sametag = NULL;
@ -350,7 +349,8 @@ void Atom::create_avec(const char *style, int narg, char **arg, char *suffix)
// if molecular system:
// atom IDs must be defined
// force atom map to be created, style will reset by map_init()
// force atom map to be created
// map style may be reset by map_init() and its call to map_style_set()
molecular = avec->molecular;
if (molecular && tag_enable == 0)
@ -480,7 +480,6 @@ void Atom::modify_params(int narg, char **arg)
if (strcmp(arg[iarg+1],"array") == 0) map_user = 1;
else if (strcmp(arg[iarg+1],"hash") == 0) map_user = 2;
else error->all(FLERR,"Illegal atom_modify command");
map_style = map_user;
iarg += 2;
} else if (strcmp(arg[iarg],"first") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal atom_modify command");

1
src/atom_map.cpp
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@ -290,6 +290,7 @@ int Atom::map_style_set()
error->all(FLERR,"Cannot create an atom map unless atoms have IDs");
// map_tag_max = max ID of any atom that will be in new map
// map_tag_max = -1 if no atoms
tagint max = -1;
for (int i = 0; i < nlocal; i++) max = MAX(max,tag[i]);

2
src/fix_wall_region.cpp
View File

@ -19,12 +19,12 @@
#include "atom_vec.h"
#include "domain.h"
#include "region.h"
#include "force.h"
#include "lattice.h"
#include "update.h"
#include "output.h"
#include "respa.h"
#include "error.h"
#include "force.h"
using namespace LAMMPS_NS;
using namespace FixConst;