Merge pull request #1730 from ohenrich/user-cgdna
USER-CGDNA quasi-unique base pairing
This commit is contained in:
Axel Kohlmeyer
@ -23,7 +23,7 @@ style1 = {hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxs
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style2 = {oxdna/excv} or {oxdna/stk} or {oxdna/hbond} or {oxdna/xstk} or {oxdna/coaxstk}
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args = list of arguments for these particular styles :ul
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{oxdna/stk} args = seq T xi kappa 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
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{oxdna/stk} args = seq T xi kappa 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
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seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
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T = temperature (oxDNA units, 0.1 = 300 K)
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xi = temperature-independent coefficient in stacking strength
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@ -36,7 +36,7 @@ args = list of arguments for these particular styles :ul
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pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
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pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
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pair_coeff * * oxdna/stk seqdep 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
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pair_coeff * * oxdna/stk seqdep 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
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pair_coeff * * oxdna/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
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pair_coeff 1 4 oxdna/hbond seqdep 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
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pair_coeff 2 3 oxdna/hbond seqdep 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
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@ -51,7 +51,10 @@ excluded volume interaction {oxdna/excv}, the stacking {oxdna/stk}, cross-stacki
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and coaxial stacking interaction {oxdna/coaxstk} as well
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as the hydrogen-bonding interaction {oxdna/hbond} between complementary pairs of nucleotides on
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opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths
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are supported "(Sulc)"_#Sulc1.
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are supported "(Sulc)"_#Sulc1. Quasi-unique base-pairing between nucleotides can be achieved by using
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more complementary pairs of atom types like 5-8 and 6-7, 9-12 and 10-11, 13-16 and 14-15, etc.
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This prevents the hybridization of in principle complementary bases within Ntypes/4 bases
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up and down along the backbone.
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The exact functional form of the pair styles is rather complex.
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The individual potentials consist of products of modulation factors,
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@ -24,7 +24,7 @@ style1 = {hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/
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style2 = {oxdna2/excv} or {oxdna2/stk} or {oxdna2/hbond} or {oxdna2/xstk} or {oxdna2/coaxstk} or {oxdna2/dh}
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args = list of arguments for these particular styles :ul
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{oxdna2/stk} args = seq T xi kappa 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
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{oxdna2/stk} args = seq T xi kappa 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
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seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
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T = temperature (oxDNA units, 0.1 = 300 K)
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xi = temperature-independent coefficient in stacking strength
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@ -41,7 +41,7 @@ args = list of arguments for these particular styles :ul
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pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
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pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
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pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
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pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
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pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
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pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
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pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
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@ -57,7 +57,10 @@ excluded volume interaction {oxdna2/excv}, the stacking {oxdna2/stk}, cross-stac
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and coaxial stacking interaction {oxdna2/coaxstk}, electrostatic Debye-Hueckel interaction {oxdna2/dh}
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as well as the hydrogen-bonding interaction {oxdna2/hbond} between complementary pairs of nucleotides on
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opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths
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are supported "(Sulc)"_#Sulc2.
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are supported "(Sulc)"_#Sulc2. Quasi-unique base-pairing between nucleotides can be achieved by using
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more complementary pairs of atom types like 5-8 and 6-7, 9-12 and 10-11, 13-16 and 14-15, etc.
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This prevents the hybridization of in principle complementary bases within Ntypes/4 bases
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up and down along the backbone.
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The exact functional form of the pair styles is rather complex.
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The individual potentials consist of products of modulation factors,
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@ -31,7 +31,7 @@ bond_coeff * 2.0 0.25 0.7525
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# oxDNA pair interactions
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pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
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pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
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pair_coeff * * oxdna/stk seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
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pair_coeff * * oxdna/stk seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
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pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
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pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
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pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
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1166
examples/USER/cgdna/examples/oxDNA/duplex1/log.07Aug19.duplex1.g++.1
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1166
examples/USER/cgdna/examples/oxDNA/duplex1/log.07Aug19.duplex1.g++.1
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1166
examples/USER/cgdna/examples/oxDNA/duplex1/log.07Aug19.duplex1.g++.4
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1166
examples/USER/cgdna/examples/oxDNA/duplex1/log.07Aug19.duplex1.g++.4
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@ -31,7 +31,7 @@ bond_coeff * 2.0 0.25 0.7525
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# oxDNA pair interactions
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pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
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pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
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pair_coeff * * oxdna/stk seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
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pair_coeff * * oxdna/stk seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
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pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
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pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
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pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
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1168
examples/USER/cgdna/examples/oxDNA/duplex2/log.07Aug19.duplex2.g++.1
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examples/USER/cgdna/examples/oxDNA/duplex2/log.07Aug19.duplex2.g++.1
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1168
examples/USER/cgdna/examples/oxDNA/duplex2/log.07Aug19.duplex2.g++.4
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1168
examples/USER/cgdna/examples/oxDNA/duplex2/log.07Aug19.duplex2.g++.4
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@ -24,14 +24,14 @@ set atom * mass 3.1575
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group all type 1 4
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# oxDNA bond interactions - FENE backbone
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# oxDNA2 bond interactions - FENE backbone
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bond_style oxdna2/fene
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bond_coeff * 2.0 0.25 0.7564
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# oxDNA pair interactions
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# oxDNA2 pair interactions
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pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
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pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
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pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
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pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
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pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
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pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
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pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
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@ -1,4 +1,4 @@
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LAMMPS (18 Jun 2019)
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LAMMPS (7 Aug 2019)
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variable number equal 1
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variable ofreq equal 1000
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variable efreq equal 1000
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@ -35,8 +35,8 @@ read_data data.duplex1
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2 = max # of 1-3 neighbors
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2 = max # of 1-4 neighbors
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4 = max # of special neighbors
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special bonds CPU = 0.000102 secs
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read_data CPU = 0.002436 secs
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special bonds CPU = 0.000116 secs
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read_data CPU = 0.002026 secs
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set atom * mass 3.1575
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10 settings made for mass
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@ -44,15 +44,15 @@ set atom * mass 3.1575
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group all type 1 4
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10 atoms in group all
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# oxDNA bond interactions - FENE backbone
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# oxDNA2 bond interactions - FENE backbone
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bond_style oxdna2/fene
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bond_coeff * 2.0 0.25 0.7564
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# oxDNA pair interactions
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# oxDNA2 pair interactions
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pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
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pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
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pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
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pair_coeff * * oxdna2/stk seqav 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
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pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
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pair_coeff * * oxdna2/stk seqav 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
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pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
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pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
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pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
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@ -135,7 +135,7 @@ Neighbor list info ...
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pair build: copy
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stencil: none
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bin: none
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Per MPI rank memory allocation (min/avg/max) = 3.023 | 3.023 | 3.023 Mbytes
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Per MPI rank memory allocation (min/avg/max) = 3.024 | 3.024 | 3.024 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0 -1.4712768 0.009525411 -1.4617514 4.663076e-06
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1000 ekin = 0.00113086229080528 | erot = 0.0043101016040658 | epot = -14.6229549982368 | etot = -14.617514034342
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@ -1139,21 +1139,21 @@ Step Temp E_pair E_mol TotEng Press
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999000 ekin = 0.190992053959174 | erot = 0.320462575795008 | epot = -15.1289686644104 | etot = -14.6175140346562
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1000000 ekin = 0.179708146665509 | erot = 0.311553394429298 | epot = -15.1087755756885 | etot = -14.6175140345937
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1000000 0.013311715 -1.5443684 0.033490821 -1.4929067 -3.7544839e-05
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Loop time of 20.4903 on 1 procs for 1000000 steps with 10 atoms
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Loop time of 18.4193 on 1 procs for 1000000 steps with 10 atoms
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Performance: 42166.322 tau/day, 48803.614 timesteps/s
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98.3% CPU use with 1 MPI tasks x no OpenMP threads
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Performance: 46907.305 tau/day, 54290.862 timesteps/s
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99.5% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 16.542 | 16.542 | 16.542 | 0.0 | 80.73
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Bond | 0.62224 | 0.62224 | 0.62224 | 0.0 | 3.04
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Pair | 14.935 | 14.935 | 14.935 | 0.0 | 81.08
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Bond | 0.55556 | 0.55556 | 0.55556 | 0.0 | 3.02
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.21974 | 0.21974 | 0.21974 | 0.0 | 1.07
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Comm | 0.16028 | 0.16028 | 0.16028 | 0.0 | 0.87
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Output | 7e-06 | 7e-06 | 7e-06 | 0.0 | 0.00
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Modify | 2.7798 | 2.7798 | 2.7798 | 0.0 | 13.57
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Other | | 0.3269 | | | 1.60
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Modify | 2.5402 | 2.5402 | 2.5402 | 0.0 | 13.79
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Other | | 0.2285 | | | 1.24
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Nlocal: 10 ave 10 max 10 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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@ -1169,4 +1169,4 @@ Neighbor list builds = 0
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Dangerous builds = 0
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#write_restart config.${number}.*
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Total wall time: 0:00:20
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Total wall time: 0:00:18
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@ -1,4 +1,4 @@
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LAMMPS (18 Jun 2019)
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LAMMPS (7 Aug 2019)
|
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variable number equal 1
|
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variable ofreq equal 1000
|
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variable efreq equal 1000
|
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@ -35,8 +35,8 @@ read_data data.duplex1
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2 = max # of 1-3 neighbors
|
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2 = max # of 1-4 neighbors
|
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4 = max # of special neighbors
|
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special bonds CPU = 0.000196 secs
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read_data CPU = 0.003266 secs
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special bonds CPU = 0.000198 secs
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read_data CPU = 0.004522 secs
|
||||
|
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set atom * mass 3.1575
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10 settings made for mass
|
||||
@ -44,15 +44,15 @@ set atom * mass 3.1575
|
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group all type 1 4
|
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10 atoms in group all
|
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|
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# oxDNA bond interactions - FENE backbone
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# oxDNA2 bond interactions - FENE backbone
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bond_style oxdna2/fene
|
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bond_coeff * 2.0 0.25 0.7564
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|
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# oxDNA pair interactions
|
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# oxDNA2 pair interactions
|
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pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
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pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/stk seqav 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/stk seqav 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
@ -135,7 +135,7 @@ Neighbor list info ...
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.652 | 7.834 | 8.016 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.653 | 7.835 | 8.018 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.4712768 0.009525411 -1.4617514 4.663076e-06
|
||||
1000 ekin = 0.00113086229080478 | erot = 0.00431010160406708 | epot = -14.6229549982368 | etot = -14.617514034342
|
||||
@ -1139,21 +1139,21 @@ Step Temp E_pair E_mol TotEng Press
|
||||
999000 ekin = 0.190992053959209 | erot = 0.320462575794744 | epot = -15.1289686644103 | etot = -14.6175140346563
|
||||
1000000 ekin = 0.179708146665587 | erot = 0.311553394428757 | epot = -15.1087755756882 | etot = -14.6175140345938
|
||||
1000000 0.013311715 -1.5443684 0.033490821 -1.4929067 -3.7544839e-05
|
||||
Loop time of 28.9854 on 4 procs for 1000000 steps with 10 atoms
|
||||
Loop time of 20.7945 on 4 procs for 1000000 steps with 10 atoms
|
||||
|
||||
Performance: 29808.075 tau/day, 34500.086 timesteps/s
|
||||
96.6% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 41549.361 tau/day, 48089.538 timesteps/s
|
||||
99.6% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.85571 | 9.8341 | 18.111 | 228.8 | 33.93
|
||||
Bond | 0.12393 | 0.38078 | 0.62324 | 32.7 | 1.31
|
||||
Pair | 0.66725 | 7.9254 | 14.304 | 209.9 | 38.11
|
||||
Bond | 0.095496 | 0.30973 | 0.49863 | 30.5 | 1.49
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 2.795 | 3.6269 | 4.4228 | 30.4 | 12.51
|
||||
Output | 1.8e-05 | 2.575e-05 | 2.9e-05 | 0.0 | 0.00
|
||||
Modify | 0.24721 | 1.1083 | 1.9206 | 64.1 | 3.82
|
||||
Other | | 14.04 | | | 48.42
|
||||
Comm | 1.8943 | 2.1825 | 2.4604 | 15.6 | 10.50
|
||||
Output | 2e-05 | 2.9e-05 | 3.2e-05 | 0.0 | 0.00
|
||||
Modify | 0.18231 | 0.95644 | 1.673 | 62.4 | 4.60
|
||||
Other | | 9.421 | | | 45.30
|
||||
|
||||
Nlocal: 2.5 ave 5 max 0 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
@ -1169,4 +1169,4 @@ Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
Total wall time: 0:00:28
|
||||
Total wall time: 0:00:20
|
||||
@ -2,6 +2,7 @@ variable number equal 2
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
variable T equal 0.1
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
@ -23,14 +24,14 @@ set atom * mass 3.1575
|
||||
|
||||
group all type 1 4
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
# oxDNA2 bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564
|
||||
|
||||
# oxDNA pair interactions
|
||||
# oxDNA2 pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
|
||||
@ -1,8 +1,9 @@
|
||||
LAMMPS (18 Jun 2019)
|
||||
LAMMPS (7 Aug 2019)
|
||||
variable number equal 2
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
variable T equal 0.1
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
@ -34,8 +35,8 @@ read_data data.duplex2
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
special bonds CPU = 0.000103 secs
|
||||
read_data CPU = 0.00215 secs
|
||||
special bonds CPU = 0.000127 secs
|
||||
read_data CPU = 0.001506 secs
|
||||
|
||||
set atom * mass 3.1575
|
||||
16 settings made for mass
|
||||
@ -43,15 +44,15 @@ set atom * mass 3.1575
|
||||
group all type 1 4
|
||||
16 atoms in group all
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
# oxDNA2 bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564
|
||||
|
||||
# oxDNA pair interactions
|
||||
# oxDNA2 pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/stk seqav 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/stk seqav 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
@ -136,7 +137,7 @@ Neighbor list info ...
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.025 | 3.025 | 3.025 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.026 | 3.026 | 3.026 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.5358787 0.0096742456 -1.5262045 1.0127369e-05
|
||||
1000 ekin = 1.54282272464468 | erot = 1.71757897250772 | epot = -24.4403527731341 | etot = -21.1799510759817
|
||||
@ -1140,21 +1141,21 @@ Step Temp E_pair E_mol TotEng Press
|
||||
999000 ekin = 2.08919327368179 | erot = 2.76364485800616 | epot = -20.9705413117635 | etot = -16.1177031800756
|
||||
1000000 ekin = 2.11761701334905 | erot = 2.1409630347026 | epot = -20.9096627221725 | etot = -16.6510826741208
|
||||
1000000 0.094116312 -1.3659956 0.059141691 -1.1745029 -3.0654283e-05
|
||||
Loop time of 43.6978 on 1 procs for 1000000 steps with 16 atoms
|
||||
Loop time of 39.73 on 1 procs for 1000000 steps with 16 atoms
|
||||
|
||||
Performance: 19772.150 tau/day, 22884.433 timesteps/s
|
||||
98.6% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
Performance: 21746.777 tau/day, 25169.881 timesteps/s
|
||||
99.7% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 32.769 | 32.769 | 32.769 | 0.0 | 74.99
|
||||
Bond | 0.93071 | 0.93071 | 0.93071 | 0.0 | 2.13
|
||||
Pair | 29.698 | 29.698 | 29.698 | 0.0 | 74.75
|
||||
Bond | 0.84677 | 0.84677 | 0.84677 | 0.0 | 2.13
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.19584 | 0.19584 | 0.19584 | 0.0 | 0.45
|
||||
Output | 1e-05 | 1e-05 | 1e-05 | 0.0 | 0.00
|
||||
Modify | 9.4507 | 9.4507 | 9.4507 | 0.0 | 21.63
|
||||
Other | | 0.3515 | | | 0.80
|
||||
Comm | 0.15576 | 0.15576 | 0.15576 | 0.0 | 0.39
|
||||
Output | 7e-06 | 7e-06 | 7e-06 | 0.0 | 0.00
|
||||
Modify | 8.7714 | 8.7714 | 8.7714 | 0.0 | 22.08
|
||||
Other | | 0.2585 | | | 0.65
|
||||
|
||||
Nlocal: 16 ave 16 max 16 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -1170,4 +1171,4 @@ Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
Total wall time: 0:00:43
|
||||
Total wall time: 0:00:39
|
||||
@ -1,8 +1,9 @@
|
||||
LAMMPS (18 Jun 2019)
|
||||
LAMMPS (7 Aug 2019)
|
||||
variable number equal 2
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
variable T equal 0.1
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
@ -34,8 +35,8 @@ read_data data.duplex2
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
special bonds CPU = 0.000162 secs
|
||||
read_data CPU = 0.002971 secs
|
||||
special bonds CPU = 0.000188 secs
|
||||
read_data CPU = 0.002335 secs
|
||||
|
||||
set atom * mass 3.1575
|
||||
16 settings made for mass
|
||||
@ -43,15 +44,15 @@ set atom * mass 3.1575
|
||||
group all type 1 4
|
||||
16 atoms in group all
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
# oxDNA2 bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564
|
||||
|
||||
# oxDNA pair interactions
|
||||
# oxDNA2 pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/stk seqav 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/stk seqav 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
@ -136,7 +137,7 @@ Neighbor list info ...
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.777 | 7.959 | 8.142 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.778 | 7.96 | 8.143 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.5358787 0.0096742456 -1.5262045 1.0127369e-05
|
||||
1000 ekin = 1.34554291364716 | erot = 2.30525041754444 | epot = -24.3924150888896 | etot = -20.741621757698
|
||||
@ -1140,21 +1141,21 @@ Step Temp E_pair E_mol TotEng Press
|
||||
999000 ekin = 2.61553981530106 | erot = 1.7387289184571 | epot = -21.0217257279766 | etot = -16.6674569942185
|
||||
1000000 ekin = 2.34012577497833 | erot = 2.86436388995813 | epot = -21.0201566044041 | etot = -15.8156669394676
|
||||
1000000 0.10400559 -1.3746133 0.060853481 -1.1675019 0.00013752759
|
||||
Loop time of 59.4195 on 4 procs for 1000000 steps with 16 atoms
|
||||
Loop time of 44.9291 on 4 procs for 1000000 steps with 16 atoms
|
||||
|
||||
Performance: 14540.686 tau/day, 16829.497 timesteps/s
|
||||
96.3% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 19230.287 tau/day, 22257.276 timesteps/s
|
||||
99.6% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.0304 | 20.212 | 37.839 | 369.5 | 34.02
|
||||
Bond | 0.12844 | 0.57006 | 0.95643 | 49.6 | 0.96
|
||||
Pair | 0.75183 | 16.839 | 31.47 | 339.4 | 37.48
|
||||
Bond | 0.10416 | 0.48181 | 0.82289 | 46.2 | 1.07
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 4.3935 | 5.5635 | 6.7052 | 44.2 | 9.36
|
||||
Output | 2.3e-05 | 3.575e-05 | 4.1e-05 | 0.0 | 0.00
|
||||
Modify | 0.3513 | 3.4695 | 6.4366 | 144.3 | 5.84
|
||||
Other | | 29.6 | | | 49.82
|
||||
Comm | 3.0032 | 3.0414 | 3.0759 | 1.7 | 6.77
|
||||
Output | 1.6e-05 | 2.2e-05 | 2.4e-05 | 0.0 | 0.00
|
||||
Modify | 0.25426 | 2.929 | 5.4956 | 134.9 | 6.52
|
||||
Other | | 21.64 | | | 48.16
|
||||
|
||||
Nlocal: 4 ave 8 max 0 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
@ -1170,4 +1171,4 @@ Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
Total wall time: 0:00:59
|
||||
Total wall time: 0:00:44
|
||||
@ -24,14 +24,14 @@ set atom * mass 1.0
|
||||
|
||||
group all type 1 4
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
# oxDNA2 bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564
|
||||
|
||||
# oxDNA pair interactions
|
||||
# oxDNA2 pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (18 Jun 2019)
|
||||
LAMMPS (7 Aug 2019)
|
||||
variable number equal 1
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
@ -35,8 +35,8 @@ read_data data.duplex3
|
||||
2 = max # of 1-3 neighbors
|
||||
2 = max # of 1-4 neighbors
|
||||
4 = max # of special neighbors
|
||||
special bonds CPU = 0.000113 secs
|
||||
read_data CPU = 0.00275 secs
|
||||
special bonds CPU = 0.000145 secs
|
||||
read_data CPU = 0.001965 secs
|
||||
|
||||
set atom * mass 1.0
|
||||
10 settings made for mass
|
||||
@ -44,15 +44,15 @@ set atom * mass 1.0
|
||||
group all type 1 4
|
||||
10 atoms in group all
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
# oxDNA2 bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564
|
||||
|
||||
# oxDNA pair interactions
|
||||
# oxDNA2 pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
@ -135,7 +135,7 @@ Neighbor list info ...
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.023 | 3.023 | 3.023 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.024 | 3.024 | 3.024 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.4720158 0.009525411 -1.4624904 3.1370518e-06
|
||||
1000 ekin = 0.00366431201929618 | erot = 0.00193726360267488 | epot = -14.630505317301 | etot = -14.624903741679
|
||||
@ -1139,21 +1139,21 @@ Step Temp E_pair E_mol TotEng Press
|
||||
999000 ekin = 0.330110494517114 | erot = 0.658973630822449 | epot = -15.6139878677246 | etot = -14.624903742385
|
||||
1000000 ekin = 0.345190458650495 | erot = 0.661138339466907 | epot = -15.6312325406154 | etot = -14.624903742498
|
||||
1000000 0.025569664 -1.5839232 0.020799898 -1.5286042 -3.5789082e-06
|
||||
Loop time of 20.5464 on 1 procs for 1000000 steps with 10 atoms
|
||||
Loop time of 25.9663 on 1 procs for 1000000 steps with 10 atoms
|
||||
|
||||
Performance: 42051.215 tau/day, 48670.388 timesteps/s
|
||||
98.3% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
Performance: 33273.840 tau/day, 38511.388 timesteps/s
|
||||
99.6% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 16.716 | 16.716 | 16.716 | 0.0 | 81.36
|
||||
Bond | 0.6285 | 0.6285 | 0.6285 | 0.0 | 3.06
|
||||
Pair | 21.428 | 21.428 | 21.428 | 0.0 | 82.52
|
||||
Bond | 0.76981 | 0.76981 | 0.76981 | 0.0 | 2.96
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.187 | 0.187 | 0.187 | 0.0 | 0.91
|
||||
Output | 6e-06 | 6e-06 | 6e-06 | 0.0 | 0.00
|
||||
Modify | 2.7186 | 2.7186 | 2.7186 | 0.0 | 13.23
|
||||
Other | | 0.2965 | | | 1.44
|
||||
Comm | 0.25709 | 0.25709 | 0.25709 | 0.0 | 0.99
|
||||
Output | 9e-06 | 9e-06 | 9e-06 | 0.0 | 0.00
|
||||
Modify | 3.1584 | 3.1584 | 3.1584 | 0.0 | 12.16
|
||||
Other | | 0.3534 | | | 1.36
|
||||
|
||||
Nlocal: 10 ave 10 max 10 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -1169,4 +1169,4 @@ Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
Total wall time: 0:00:20
|
||||
Total wall time: 0:00:25
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (18 Jun 2019)
|
||||
LAMMPS (7 Aug 2019)
|
||||
variable number equal 1
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
@ -35,8 +35,8 @@ read_data data.duplex3
|
||||
2 = max # of 1-3 neighbors
|
||||
2 = max # of 1-4 neighbors
|
||||
4 = max # of special neighbors
|
||||
special bonds CPU = 0.000189 secs
|
||||
read_data CPU = 0.003302 secs
|
||||
special bonds CPU = 0.000188 secs
|
||||
read_data CPU = 0.002791 secs
|
||||
|
||||
set atom * mass 1.0
|
||||
10 settings made for mass
|
||||
@ -44,15 +44,15 @@ set atom * mass 1.0
|
||||
group all type 1 4
|
||||
10 atoms in group all
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
# oxDNA2 bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564
|
||||
|
||||
# oxDNA pair interactions
|
||||
# oxDNA2 pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
@ -135,7 +135,7 @@ Neighbor list info ...
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.652 | 7.834 | 8.016 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.653 | 7.835 | 8.018 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.4720158 0.009525411 -1.4624904 3.1370518e-06
|
||||
1000 ekin = 0.00366431201929595 | erot = 0.00193726360268106 | epot = -14.630505317301 | etot = -14.624903741679
|
||||
@ -1139,21 +1139,21 @@ Step Temp E_pair E_mol TotEng Press
|
||||
999000 ekin = 0.330110494517446 | erot = 0.658973630822486 | epot = -15.613987867725 | etot = -14.6249037423851
|
||||
1000000 ekin = 0.345190458651126 | erot = 0.66113833946702 | epot = -15.6312325406162 | etot = -14.624903742498
|
||||
1000000 0.025569664 -1.5839232 0.020799898 -1.5286042 -3.5789082e-06
|
||||
Loop time of 30.1999 on 4 procs for 1000000 steps with 10 atoms
|
||||
Loop time of 20.0167 on 4 procs for 1000000 steps with 10 atoms
|
||||
|
||||
Performance: 28609.339 tau/day, 33112.661 timesteps/s
|
||||
96.4% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 43164.007 tau/day, 49958.342 timesteps/s
|
||||
99.5% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.90762 | 10.291 | 18.476 | 234.3 | 34.08
|
||||
Bond | 0.11783 | 0.39332 | 0.61914 | 34.0 | 1.30
|
||||
Pair | 0.59089 | 7.5652 | 13.908 | 205.5 | 37.79
|
||||
Bond | 0.090803 | 0.29363 | 0.47758 | 29.6 | 1.47
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 2.8711 | 3.8042 | 4.7159 | 34.0 | 12.60
|
||||
Output | 2e-05 | 3.15e-05 | 3.6e-05 | 0.0 | 0.00
|
||||
Modify | 0.27052 | 1.1583 | 1.9428 | 63.9 | 3.84
|
||||
Other | | 14.55 | | | 48.19
|
||||
Comm | 1.7298 | 2.0312 | 2.2983 | 16.6 | 10.15
|
||||
Output | 1.4e-05 | 2.075e-05 | 2.3e-05 | 0.0 | 0.00
|
||||
Modify | 0.17638 | 0.90613 | 1.5893 | 60.1 | 4.53
|
||||
Other | | 9.22 | | | 46.06
|
||||
|
||||
Nlocal: 2.5 ave 5 max 0 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
@ -1169,4 +1169,4 @@ Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
Total wall time: 0:00:30
|
||||
Total wall time: 0:00:20
|
||||
@ -33,20 +33,36 @@
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace MFOxdna;
|
||||
|
||||
// sequence-specific base-pairing strength
|
||||
// A:0 C:1 G:2 T:3, 5'- (i,j) -3'
|
||||
static const double alpha_hb[4][4] =
|
||||
{{1.00000,1.00000,1.00000,0.82915},
|
||||
{1.00000,1.00000,1.15413,1.00000},
|
||||
{1.00000,1.15413,1.00000,1.00000},
|
||||
{0.82915,1.00000,1.00000,1.00000}};
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairOxdnaHbond::PairOxdnaHbond(LAMMPS *lmp) : Pair(lmp)
|
||||
{
|
||||
single_enable = 0;
|
||||
writedata = 1;
|
||||
|
||||
// sequence-specific base-pairing strength
|
||||
// A:0 C:1 G:2 T:3, 5'- [i][j] -3'
|
||||
|
||||
alpha_hb[0][0] = 1.00000;
|
||||
alpha_hb[0][1] = 1.00000;
|
||||
alpha_hb[0][2] = 1.00000;
|
||||
alpha_hb[0][3] = 0.82915;
|
||||
|
||||
alpha_hb[1][0] = 1.00000;
|
||||
alpha_hb[1][1] = 1.00000;
|
||||
alpha_hb[1][2] = 1.15413;
|
||||
alpha_hb[1][3] = 1.00000;
|
||||
|
||||
alpha_hb[2][0] = 1.00000;
|
||||
alpha_hb[2][1] = 1.15413;
|
||||
alpha_hb[2][2] = 1.00000;
|
||||
alpha_hb[2][3] = 1.00000;
|
||||
|
||||
alpha_hb[3][0] = 0.82915;
|
||||
alpha_hb[3][1] = 1.00000;
|
||||
alpha_hb[3][2] = 1.00000;
|
||||
alpha_hb[3][3] = 1.00000;
|
||||
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -617,7 +633,7 @@ void PairOxdnaHbond::coeff(int narg, char **arg)
|
||||
if (narg != 27) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/hbond");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo,ihi,jlo,jhi;
|
||||
int ilo,ihi,jlo,jhi,imod4,jmod4;
|
||||
force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
|
||||
force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
|
||||
|
||||
@ -730,8 +746,13 @@ void PairOxdnaHbond::coeff(int narg, char **arg)
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
for (int j = MAX(jlo,i); j <= jhi; j++) {
|
||||
|
||||
imod4 = i%4;
|
||||
if (imod4 == 0) imod4 = 4;
|
||||
jmod4 = j%4;
|
||||
if (jmod4 == 0) jmod4 = 4;
|
||||
|
||||
epsilon_hb[i][j] = epsilon_hb_one;
|
||||
if (seqdepflag) epsilon_hb[i][j] *= alpha_hb[i-1][j-1];
|
||||
if (seqdepflag) epsilon_hb[i][j] *= alpha_hb[imod4-1][jmod4-1];
|
||||
a_hb[i][j] = a_hb_one;
|
||||
cut_hb_0[i][j] = cut_hb_0_one;
|
||||
cut_hb_c[i][j] = cut_hb_c_one;
|
||||
@ -742,7 +763,7 @@ void PairOxdnaHbond::coeff(int narg, char **arg)
|
||||
b_hb_lo[i][j] = b_hb_lo_one;
|
||||
b_hb_hi[i][j] = b_hb_hi_one;
|
||||
shift_hb[i][j] = shift_hb_one;
|
||||
if (seqdepflag) shift_hb[i][j] *= alpha_hb[i-1][j-1];
|
||||
if (seqdepflag) shift_hb[i][j] *= alpha_hb[imod4-1][jmod4-1];
|
||||
|
||||
a_hb1[i][j] = a_hb1_one;
|
||||
theta_hb1_0[i][j] = theta_hb1_0_one;
|
||||
@ -821,6 +842,7 @@ void PairOxdnaHbond::init_list(int id, NeighList *ptr)
|
||||
|
||||
double PairOxdnaHbond::init_one(int i, int j)
|
||||
{
|
||||
int imod4,jmod4;
|
||||
|
||||
if (setflag[i][j] == 0) {
|
||||
error->all(FLERR,"Coefficient mixing not defined in oxDNA");
|
||||
@ -829,8 +851,13 @@ double PairOxdnaHbond::init_one(int i, int j)
|
||||
error->all(FLERR,"Offset not supported in oxDNA");
|
||||
}
|
||||
|
||||
imod4 = i%4;
|
||||
if (imod4 == 0) imod4 = 4;
|
||||
jmod4 = j%4;
|
||||
if (jmod4 == 0) jmod4 = 4;
|
||||
|
||||
if (seqdepflag) {
|
||||
epsilon_hb[j][i] = epsilon_hb[i][j] / alpha_hb[i-1][j-1] * alpha_hb[j-1][i-1];
|
||||
epsilon_hb[j][i] = epsilon_hb[i][j] / alpha_hb[imod4-1][jmod4-1] * alpha_hb[jmod4-1][imod4-1];
|
||||
}
|
||||
else {
|
||||
epsilon_hb[j][i] = epsilon_hb[i][j];
|
||||
@ -845,7 +872,7 @@ double PairOxdnaHbond::init_one(int i, int j)
|
||||
cut_hb_lc[j][i] = cut_hb_lc[i][j];
|
||||
cut_hb_hc[j][i] = cut_hb_hc[i][j];
|
||||
if (seqdepflag) {
|
||||
shift_hb[j][i] = shift_hb[i][j] / alpha_hb[i-1][j-1] * alpha_hb[j-1][i-1];
|
||||
shift_hb[j][i] = shift_hb[i][j] / alpha_hb[imod4-1][jmod4-1] * alpha_hb[jmod4-1][imod4-1];
|
||||
}
|
||||
else {
|
||||
shift_hb[j][i] = shift_hb[i][j];
|
||||
|
||||
@ -45,6 +45,7 @@ class PairOxdnaHbond : public Pair {
|
||||
|
||||
protected:
|
||||
// h-bonding interaction
|
||||
double alpha_hb[4][4];
|
||||
double **epsilon_hb, **a_hb, **cut_hb_0, **cut_hb_c, **cut_hb_lo, **cut_hb_hi;
|
||||
double **cut_hb_lc, **cut_hb_hc, **b_hb_lo, **b_hb_hi, **shift_hb;
|
||||
double **cutsq_hb_hc;
|
||||
|
||||
@ -33,20 +33,36 @@
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace MFOxdna;
|
||||
|
||||
// sequence-specific stacking strength
|
||||
// A:0 C:1 G:2 T:3, 5'- (i,j) -3'
|
||||
static const double eta_st[4][4] =
|
||||
{{1.11960,1.00852,0.96950,0.99632},
|
||||
{1.01889,0.97804,1.02681,0.96950},
|
||||
{0.98169,1.05913,0.97804,1.00852},
|
||||
{0.94694,0.98169,1.01889,0.96383}};
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairOxdnaStk::PairOxdnaStk(LAMMPS *lmp) : Pair(lmp)
|
||||
{
|
||||
single_enable = 0;
|
||||
writedata = 1;
|
||||
|
||||
// sequence-specific stacking strength
|
||||
// A:0 C:1 G:2 T:3, 5'- [i][j] -3'
|
||||
|
||||
eta_st[0][0] = 1.11960;
|
||||
eta_st[0][1] = 1.00852;
|
||||
eta_st[0][2] = 0.96950;
|
||||
eta_st[0][3] = 0.99632;
|
||||
|
||||
eta_st[1][0] = 1.01889;
|
||||
eta_st[1][1] = 0.97804;
|
||||
eta_st[1][2] = 1.02681;
|
||||
eta_st[1][3] = 0.96950;
|
||||
|
||||
eta_st[2][0] = 0.98169;
|
||||
eta_st[2][1] = 1.05913;
|
||||
eta_st[2][2] = 0.97804;
|
||||
eta_st[2][3] = 1.00852;
|
||||
|
||||
eta_st[3][0] = 0.94694;
|
||||
eta_st[3][1] = 0.98169;
|
||||
eta_st[3][2] = 1.01889;
|
||||
eta_st[3][3] = 0.96383;
|
||||
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -762,7 +778,7 @@ void PairOxdnaStk::coeff(int narg, char **arg)
|
||||
if (narg != 24) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/stk");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo,ihi,jlo,jhi;
|
||||
int ilo,ihi,jlo,jhi,imod4,jmod4;
|
||||
force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
|
||||
force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
|
||||
|
||||
@ -853,16 +869,21 @@ void PairOxdnaStk::coeff(int narg, char **arg)
|
||||
dtheta_st6_c_one = 1/(a_st6_one*dtheta_st6_ast_one);
|
||||
|
||||
b_st1_one = a_st1_one*a_st1_one*cosphi_st1_ast_one*cosphi_st1_ast_one/(1-a_st1_one*cosphi_st1_ast_one*cosphi_st1_ast_one);
|
||||
cosphi_st1_c_one=1/(a_st1_one*cosphi_st1_ast_one);
|
||||
cosphi_st1_c_one = 1/(a_st1_one*cosphi_st1_ast_one);
|
||||
|
||||
b_st2_one = a_st2_one*a_st2_one*cosphi_st2_ast_one*cosphi_st2_ast_one/(1-a_st2_one*cosphi_st2_ast_one*cosphi_st2_ast_one);
|
||||
cosphi_st2_c_one=1/(a_st2_one*cosphi_st2_ast_one);
|
||||
cosphi_st2_c_one = 1/(a_st2_one*cosphi_st2_ast_one);
|
||||
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
for (int j = MAX(jlo,i); j <= jhi; j++) {
|
||||
|
||||
imod4 = i%4;
|
||||
if (imod4 == 0) imod4 = 4;
|
||||
jmod4 = j%4;
|
||||
if (jmod4 == 0) jmod4 = 4;
|
||||
|
||||
epsilon_st[i][j] = epsilon_st_one;
|
||||
if (seqdepflag) epsilon_st[i][j] *= eta_st[i-1][j-1];
|
||||
if (seqdepflag) epsilon_st[i][j] *= eta_st[imod4-1][jmod4-1];
|
||||
a_st[i][j] = a_st_one;
|
||||
cut_st_0[i][j] = cut_st_0_one;
|
||||
cut_st_c[i][j] = cut_st_c_one;
|
||||
@ -873,7 +894,7 @@ void PairOxdnaStk::coeff(int narg, char **arg)
|
||||
b_st_lo[i][j] = b_st_lo_one;
|
||||
b_st_hi[i][j] = b_st_hi_one;
|
||||
shift_st[i][j] = shift_st_one;
|
||||
if (seqdepflag) shift_st[i][j] *= eta_st[i-1][j-1];
|
||||
if (seqdepflag) shift_st[i][j] *= eta_st[imod4-1][jmod4-1];
|
||||
|
||||
a_st4[i][j] = a_st4_one;
|
||||
theta_st4_0[i][j] = theta_st4_0_one;
|
||||
@ -945,6 +966,8 @@ void PairOxdnaStk::init_list(int id, NeighList *ptr)
|
||||
double PairOxdnaStk::init_one(int i, int j)
|
||||
{
|
||||
|
||||
int imod4,jmod4;
|
||||
|
||||
if (setflag[i][j] == 0) {
|
||||
error->all(FLERR,"Coefficient mixing not defined in oxDNA");
|
||||
}
|
||||
@ -952,8 +975,13 @@ double PairOxdnaStk::init_one(int i, int j)
|
||||
error->all(FLERR,"Offset not supported in oxDNA");
|
||||
}
|
||||
|
||||
imod4 = i%4;
|
||||
if (imod4 == 0) imod4 = 4;
|
||||
jmod4 = j%4;
|
||||
if (jmod4 == 0) jmod4 = 4;
|
||||
|
||||
if (seqdepflag) {
|
||||
epsilon_st[j][i] = epsilon_st[i][j] / eta_st[i-1][j-1] * eta_st[j-1][i-1];
|
||||
epsilon_st[j][i] = epsilon_st[i][j] / eta_st[imod4-1][jmod4-1] * eta_st[jmod4-1][imod4-1];
|
||||
}
|
||||
else {
|
||||
epsilon_st[j][i] = epsilon_st[i][j];
|
||||
@ -968,7 +996,7 @@ double PairOxdnaStk::init_one(int i, int j)
|
||||
cut_st_lc[j][i] = cut_st_lc[i][j];
|
||||
cut_st_hc[j][i] = cut_st_hc[i][j];
|
||||
if (seqdepflag) {
|
||||
shift_st[j][i] = shift_st[i][j] / eta_st[i-1][j-1] * eta_st[j-1][i-1];
|
||||
shift_st[j][i] = shift_st[i][j] / eta_st[imod4-1][jmod4-1] * eta_st[jmod4-1][imod4-1];
|
||||
}
|
||||
else {
|
||||
shift_st[j][i] = shift_st[i][j];
|
||||
|
||||
@ -45,6 +45,7 @@ class PairOxdnaStk : public Pair {
|
||||
|
||||
protected:
|
||||
// stacking interaction
|
||||
double eta_st[4][4];
|
||||
double stacking_strength(double, double, double);
|
||||
double **epsilon_st, **a_st, **cut_st_0, **cut_st_c;
|
||||
double **cut_st_lo, **cut_st_hi;
|
||||
|
||||
Reference in New Issue
Block a user