Merge branch 'master' into collected-small-changes

doc/src/bond_oxdna.rst

@@ -84,6 +84,13 @@ commands:
    the bond topology in the data file. The first (second) atom in a bond definition
    is understood to point towards the 3'-end (5'-end) of the strand.
 
+.. warning::
+
+   If data files are produced with :doc:`write_data <write_data>`, then the
+   :doc:`newton <newton>` command should be set to *newton on* or *newton off on*.
+   Otherwise the data files will not have the same 3'-to-5' polarity as the
+   initial data file. This limitation does not apply to binary restart files
+   produced with :doc:`write_restart <write_restart>`.
 
 Example input and data files for DNA and RNA duplexes can be found in
 examples/PACKAGES/cgdna/examples/oxDNA/ , /oxDNA2/ and /oxRNA2/.  A simple python

examples/PACKAGES/cgdna/README

@@ -72,6 +72,14 @@ between two individual nucleotides can be established.
 
 /******************************************************************************/
 
+/examples/oxDNA2/dsring:
+
+This example uses a dsDNA ring of 74 base pairs. The bonds which close the ring 
+are (in 3' to 5' direction) between nucleotide 74 and 1 and between nucleotide 
+148 and 75, respectively. 
+
+/******************************************************************************/
+
 /examples/oxRNA2/duplex2
 
 This example uses the duplex2 with the oxRNA2 force field instead of oxDNA or 

examples/PACKAGES/cgdna/examples/oxDNA/duplex1/in.duplex1

@@ -7,7 +7,7 @@ units lj
 
 dimension 3
 
-newton off
+newton on
 
 boundary  p p p
 
@@ -67,3 +67,4 @@ dump_modify out format line "%d %d %d  %22.15le %22.15le %22.15le  %d %d %d  %22
 run 1000000
 
 write_data last_config.${number}.* nocoeff
+#write_restart last_config.${number}.*

examples/PACKAGES/cgdna/examples/oxDNA/duplex2/in.duplex2

@@ -7,7 +7,7 @@ units lj
 
 dimension 3
 
-newton off
+newton on
 
 boundary  p p p
 
@@ -67,3 +67,4 @@ dump_modify out format line "%d %d %d  %22.15le %22.15le %22.15le  %d %d %d  %22
 run 1000000
 
 write_data last_config.${number}.* nocoeff
+#write_restart last_config.${number}.*

examples/PACKAGES/cgdna/examples/oxDNA2/dsring/data.dsring

@@ -0,0 +1,622 @@
+LAMMPS data file via write_data, version 2 Jul 2021
+
+148 atoms
+4 atom types
+148 bonds
+1 bond types
+148 ellipsoids
+
+0 100 xlo xhi
+0 100 ylo yhi
+0 100 zlo zhi
+
+Masses
+
+1 3.1575
+2 3.1575
+3 3.1575
+4 3.1575
+
+Atoms # hybrid
+
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+Velocities
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+99 1.173984503142341 1.173984503142341 1.173984503142341 0.2468582232791126 0.49224626821105333 0.30309532857077576 0.7777453637472519
+100 1.173984503142341 1.173984503142341 1.173984503142341 -0.03380456035420594 0.5634460183047242 0.08545990308043122 0.8210252378101995
+101 1.173984503142341 1.173984503142341 1.173984503142341 -0.26750916515001516 0.4857064004847054 0.009320517332115886 0.8321305588942125
+102 1.173984503142341 1.173984503142341 1.173984503142341 -0.543656333310932 0.3668193234682623 -0.09381801460790738 0.7490524382953638
+103 1.173984503142341 1.173984503142341 1.173984503142341 0.7108784431095552 -0.3004632412363646 0.2190205688208185 -0.5969955361820375
+104 1.173984503142341 1.173984503142341 1.173984503142341 0.8734231811131953 -0.14399683070372168 0.19737468070828412 -0.4212363883340244
+105 1.173984503142341 1.173984503142341 1.173984503142341 0.9684624161954964 -0.105190045875246 0.17391545136610614 -0.14411460176424984
+106 1.173984503142341 1.173984503142341 1.173984503142341 0.9799304485597246 0.037984124779449666 0.14105544742949488 0.13563510976418097
+107 1.173984503142341 1.173984503142341 1.173984503142341 0.8816175546504624 0.20405639480623733 0.14071717244217888 0.40163435168159917
+108 1.173984503142341 1.173984503142341 1.173984503142341 0.6668815181201708 0.2184913756962591 0.13935946384415568 0.6986483374152993
+109 1.173984503142341 1.173984503142341 1.173984503142341 0.49523667831069 0.06959764035843413 0.04878276823652622 0.8645906791282876
+110 1.173984503142341 1.173984503142341 1.173984503142341 0.2207732329238526 -0.06373893139772668 0.037699540120053256 0.9725097803741426
+111 1.173984503142341 1.173984503142341 1.173984503142341 -0.032729617987676665 -0.18237738709355036 0.08976233597699147 0.9785754870337106
+112 1.173984503142341 1.173984503142341 1.173984503142341 -0.15032793635914565 -0.23367266896015637 0.20496632388946223 0.9385027444830824
+113 1.173984503142341 1.173984503142341 1.173984503142341 0.5098818708103572 0.17022830741237596 -0.2655328085989286 -0.8003343855739379
+114 1.173984503142341 1.173984503142341 1.173984503142341 0.7386002630722802 0.13150233806957554 -0.2899184849443961 -0.5942424240655826
+115 1.173984503142341 1.173984503142341 1.173984503142341 0.8183885516845668 0.21176889551544467 -0.29030250974778893 -0.44846244680902864
+116 1.173984503142341 1.173984503142341 1.173984503142341 0.9430612626489262 0.10580295822334976 -0.2990836107868347 -0.09995090135116472
+117 1.173984503142341 1.173984503142341 1.173984503142341 0.9613379941508746 0.03141943836189481 -0.22153618567675704 0.16051105360936818
+118 1.173984503142341 1.173984503142341 1.173984503142341 0.8625667911488177 0.009442517727487543 -0.19942173035959687 0.46488745210704746
+119 1.173984503142341 1.173984503142341 1.173984503142341 0.7259073589630057 -0.13376476050843852 -0.17209740381142 0.6523403855740064
+120 1.173984503142341 1.173984503142341 1.173984503142341 0.5281310594886722 -0.2846679630342966 -0.07506778574311505 0.7964964296021063
+121 1.173984503142341 1.173984503142341 1.173984503142341 0.24241907358145395 -0.3683073657243024 0.039055584363879806 0.8966924436210727
+122 1.173984503142341 1.173984503142341 1.173984503142341 -0.044981165612273756 -0.40529534424684105 0.1971478516389492 0.8915408589998233
+123 1.173984503142341 1.173984503142341 1.173984503142341 -0.3495232584251298 -0.40209106895373176 0.34714827984449365 0.7717799789373487
+124 1.173984503142341 1.173984503142341 1.173984503142341 0.5344020410886484 0.3826673897545711 -0.38492167218812157 -0.6479316581080214
+125 1.173984503142341 1.173984503142341 1.173984503142341 0.7053269695515239 0.29260497262472956 -0.500965349977395 -0.40734495718073077
+126 1.173984503142341 1.173984503142341 1.173984503142341 0.7696439701870998 0.21424045744249637 -0.5824916559487316 -0.1498421045620125
+127 1.173984503142341 1.173984503142341 1.173984503142341 0.7423816103336222 0.1139330316098165 -0.6216492250908265 0.22235343462746351
+128 1.173984503142341 1.173984503142341 1.173984503142341 0.5887700508646756 -0.08843642096111673 -0.6840133892265956 0.4214908184185525
+129 1.173984503142341 1.173984503142341 1.173984503142341 0.453096146271983 -0.38728607571982976 -0.6241259420947486 0.5051536263270361
+130 1.173984503142341 1.173984503142341 1.173984503142341 -0.4409693358675804 0.53279196704852 0.4417418096721996 -0.5714393565905346
+131 1.173984503142341 1.173984503142341 1.173984503142341 -0.18566644236274712 0.6770317752573873 0.25184635469644123 -0.6661301382600142
+132 1.173984503142341 1.173984503142341 1.173984503142341 0.015608637060561658 0.7425789407541207 -0.020406929491472138 -0.6692656008090734
+133 1.173984503142341 1.173984503142341 1.173984503142341 0.08018393872270876 0.7828265827838332 -0.23834222384166942 -0.5691625967964753
+134 1.173984503142341 1.173984503142341 1.173984503142341 0.13194668226893702 0.7589329168513657 -0.46681103776605365 -0.43439424003717964
+135 1.173984503142341 1.173984503142341 1.173984503142341 0.23078479216727615 0.7124321296591045 -0.5847273355040361 -0.31188585002858094
+136 1.173984503142341 1.173984503142341 1.173984503142341 -0.25136284638005546 -0.45701375225575186 0.841389844073701 0.14148597103058816
+137 1.173984503142341 1.173984503142341 1.173984503142341 -0.33882629405552384 -0.365928882584538 0.8652581637618377 0.05119673222505744
+138 1.173984503142341 1.173984503142341 1.173984503142341 -0.3901032217728516 -0.04271905647523107 0.919195929073709 -0.03276282269018462
+139 1.173984503142341 1.173984503142341 1.173984503142341 -0.3503464321192356 0.2164507057056595 0.8846466649907219 -0.21864754199770353
+140 1.173984503142341 1.173984503142341 1.173984503142341 -0.2714234139641493 0.5100075547669219 0.7525252671110235 -0.3161128703362045
+141 1.173984503142341 1.173984503142341 1.173984503142341 -0.18623801902606954 0.7425995746707363 0.5393607888180064 -0.35064399531961904
+142 1.173984503142341 1.173984503142341 1.173984503142341 -0.20986530401416495 0.8687694482447833 0.31310815046609125 -0.3211845047308489
+143 1.173984503142341 1.173984503142341 1.173984503142341 -0.1354858154681459 0.9418151150282347 0.014007263864675714 -0.3072973795370049
+144 1.173984503142341 1.173984503142341 1.173984503142341 -0.09121534676964865 0.942226022288734 -0.27543028841845296 -0.16741576884323378
+145 1.173984503142341 1.173984503142341 1.173984503142341 -0.07761809459687324 0.8625267258049417 -0.49537475942792236 -0.06802151413402847
+146 1.173984503142341 1.173984503142341 1.173984503142341 -0.07853628249634757 0.6763776292711046 -0.7295609015799718 -0.06392375019562685
+147 1.173984503142341 1.173984503142341 1.173984503142341 0.18414802295685903 -0.34920401662445405 0.9187682994180332 0.0032973320918147885
+148 1.173984503142341 1.173984503142341 1.173984503142341 0.13019081328575915 -0.1370605858009623 0.9781659097238085 -0.08634929652338917

examples/PACKAGES/cgdna/examples/oxDNA2/dsring/in.dsring

@@ -0,0 +1,72 @@
+variable number	equal 5
+variable ofreq	equal 1000
+variable efreq	equal 1000
+variable T      equal 0.1
+variable rhos   equal 0.2
+
+units lj
+
+dimension 3
+
+newton on
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid oxdna
+atom_modify sort 0 1.0
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 2.0 bin
+neigh_modify every 1 delay 0 check yes
+
+read_data data.dsring
+
+set atom * mass 3.1575
+
+group all type 1 4
+
+# oxDNA2 bond interactions - FENE backbone
+bond_style oxdna2/fene
+bond_coeff * 2.0 0.25 0.7564
+special_bonds lj 0 1 1
+
+# 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 0.75 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
+pair_coeff * * oxdna2/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 
+pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
+pair_coeff * * oxdna2/dh      ${T} ${rhos} 0.815
+
+# NVE ensemble
+fix 1 all nve/asphere
+#fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10
+
+timestep 1e-5
+
+#comm_style tiled
+fix 3 all balance 1000 1.03 shift xyz 10 1.03
+comm_modify cutoff 3.8
+
+compute quat all property/atom quatw quati quatj quatk
+
+compute erot all erotate/asphere
+compute ekin all ke
+compute epot all pe
+variable erot equal c_erot
+variable ekin equal c_ekin
+variable epot equal c_epot
+variable etot equal c_erot+c_ekin+c_epot
+fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+
+dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
+dump_modify out sort id
+dump_modify out format line "%d %d %d  %22.15le %22.15le %22.15le  %d %d %d  %22.15le %22.15le %22.15le  %22.15le %22.15le %22.15le %22.15le  %22.15le %22.15le %22.15le"
+
+run 100000
+
+write_data last_config.${number}.* nocoeff
+#write_restart last_config.${number}.*

examples/PACKAGES/cgdna/examples/oxDNA2/dsring/log.2Jul21.dsring.g++.1

@@ -0,0 +1,281 @@
+LAMMPS (2 Jul 2021)
+variable number	equal 5
+variable ofreq	equal 1000
+variable efreq	equal 1000
+variable T      equal 0.1
+variable rhos   equal 0.2
+
+units lj
+
+dimension 3
+
+newton on
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid oxdna
+WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:157)
+atom_modify sort 0 1.0
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 2.0 bin
+neigh_modify every 1 delay 0 check yes
+
+read_data data.dsring
+Reading data file ...
+  orthogonal box = (0.0000000 0.0000000 0.0000000) to (100.00000 100.00000 100.00000)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  148 atoms
+  reading velocities ...
+  148 velocities
+  scanning bonds ...
+  1 = max bonds/atom
+  148 ellipsoids
+  reading bonds ...
+  148 bonds
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     2 = max # of 1-2 neighbors
+     2 = max # of 1-3 neighbors
+     4 = max # of 1-4 neighbors
+     6 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
+  read_data CPU = 0.004 seconds
+
+set atom * mass 3.1575
+Setting atom values ...
+  148 settings made for mass
+
+group all type 1 4
+148 atoms in group all
+
+# oxDNA2 bond interactions - FENE backbone
+bond_style oxdna2/fene
+bond_coeff * 2.0 0.25 0.7564
+special_bonds lj 0 1 1
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        1        1       
+  special bond factors coul:  0        0        0       
+     2 = max # of 1-2 neighbors
+     2 = max # of 1-3 neighbors
+     4 = max # of 1-4 neighbors
+     6 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
+
+# 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 0.75 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
+pair_coeff * * oxdna2/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
+pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
+pair_coeff * * oxdna2/dh      ${T} ${rhos} 0.815
+pair_coeff * * oxdna2/dh      0.1 ${rhos} 0.815
+pair_coeff * * oxdna2/dh      0.1 0.2 0.815
+
+# NVE ensemble
+fix 1 all nve/asphere
+#fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10
+
+timestep 1e-5
+
+#comm_style tiled
+fix 3 all balance 1000 1.03 shift xyz 10 1.03
+comm_modify cutoff 3.8
+
+compute quat all property/atom quatw quati quatj quatk
+
+compute erot all erotate/asphere
+compute ekin all ke
+compute epot all pe
+variable erot equal c_erot
+variable ekin equal c_ekin
+variable epot equal c_epot
+variable etot equal c_erot+c_ekin+c_epot
+fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+fix 5 all print 1000 "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+
+dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
+dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
+dump out all custom 1000 out.5.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
+dump_modify out sort id
+dump_modify out format line "%d %d %d  %22.15le %22.15le %22.15le  %d %d %d  %22.15le %22.15le %22.15le  %22.15le %22.15le %22.15le %22.15le  %22.15le %22.15le %22.15le"
+
+run 100000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.6389877
+  ghost atom cutoff = 5.6389877
+  binsize = 2.8194939, bins = 36 36 36
+  5 neighbor lists, perpetual/occasional/extra = 5 0 0
+  (1) pair oxdna2/excv, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+  (2) pair oxdna2/hbond, perpetual, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (3) pair oxdna2/xstk, perpetual, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (4) pair oxdna2/coaxstk, perpetual, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (5) pair oxdna2/dh, perpetual, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+WARNING: Communication cutoff adjusted to 5.638987723814632 (../comm.cpp:739)
+0  ekin = 20.4724634226502 |  erot = 21.0406985312466 | epot = -222.283862600785 | etot = -180.770700646889
+Per MPI rank memory allocation (min/avg/max) = 9.601 | 9.601 | 9.601 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume 
+       0  0.092845639   -1.5501211   0.04820308   -1.3635905 -9.0052368e-06      1000000 
+1000  ekin = 20.531989141805 |  erot = 21.2158633183735 | epot = -222.518553109361 | etot = -180.770700649183
+2000  ekin = 20.585620972069 |  erot = 21.391859435226 | epot = -222.748181058335 | etot = -180.77070065104
+3000  ekin = 20.6239332104642 |  erot = 21.5529389082728 | epot = -222.947572771312 | etot = -180.770700652575
+4000  ekin = 20.6395549184482 |  erot = 21.6854113323895 | epot = -223.095666904229 | etot = -180.770700653391
+5000  ekin = 20.6295551742564 |  erot = 21.7809539301805 | epot = -223.181209757876 | etot = -180.770700653439
+6000  ekin = 20.5959625511847 |  erot = 21.8369756530727 | epot = -223.203638857302 | etot = -180.770700653045
+7000  ekin = 20.5431034482068 |  erot = 21.8556844173875 | epot = -223.169488517716 | etot = -180.770700652122
+8000  ekin = 20.4774701419092 |  erot = 21.8437134145374 | epot = -223.091884207389 | etot = -180.770700650943
+9000  ekin = 20.4074566554238 |  erot = 21.8097283692398 | epot = -222.987885674261 | etot = -180.770700649597
+10000  ekin = 20.3427303660296 |  erot = 21.7629575866663 | epot = -222.876388600948 | etot = -180.770700648253
+11000  ekin = 20.2927407149577 |  erot = 21.7112100845349 | epot = -222.774651446682 | etot = -180.770700647189
+12000  ekin = 20.2665977502213 |  erot = 21.6594999867139 | epot = -222.696798383221 | etot = -180.770700646286
+13000  ekin = 20.2733920359447 |  erot = 21.6092715397932 | epot = -222.653364221616 | etot = -180.770700645878
+14000  ekin = 20.319652478907 |  erot = 21.558663097499 | epot = -222.649016222075 | etot = -180.770700645669
+15000  ekin = 20.4104009374291 |  erot = 21.5031572556304 | epot = -222.684258838857 | etot = -180.770700645798
+16000  ekin = 20.5472869005793 |  erot = 21.4346177247038 | epot = -222.752605272036 | etot = -180.770700646753
+17000  ekin = 20.7266657908775 |  erot = 21.3426631585214 | epot = -222.840029597232 | etot = -180.770700647833
+18000  ekin = 20.9417612759981 |  erot = 21.2178611180923 | epot = -222.930323042997 | etot = -180.770700648907
+19000  ekin = 21.1819308659399 |  erot = 21.0532289630289 | epot = -223.00586047892 | etot = -180.770700649951
+20000  ekin = 21.4358169889477 |  erot = 20.8473069564703 | epot = -223.053824595387 | etot = -180.770700649969
+21000  ekin = 21.6968513751 |  erot = 20.6066744652581 | epot = -223.074226489837 | etot = -180.770700649478
+22000  ekin = 21.9614458442786 |  erot = 20.3429420444505 | epot = -223.07508853737 | etot = -180.770700648641
+23000  ekin = 22.2276099755705 |  erot = 20.0703385165238 | epot = -223.068649139875 | etot = -180.77070064778
+24000  ekin = 22.4935893196675 |  erot = 19.802067172166 | epot = -223.066357139276 | etot = -180.770700647443
+25000  ekin = 22.7566064548228 |  erot = 19.5464828008836 | epot = -223.073789902975 | etot = -180.770700647269
+26000  ekin = 23.0126717548399 |  erot = 19.3065017718462 | epot = -223.089874174571 | etot = -180.770700647885
+27000  ekin = 23.2550417060594 |  erot = 19.0797753474567 | epot = -223.105517701932 | etot = -180.770700648416
+28000  ekin = 23.4774329734805 |  erot = 18.8646197299574 | epot = -223.112753352067 | etot = -180.770700648629
+29000  ekin = 23.6747927720663 |  erot = 18.6628653411825 | epot = -223.108358761693 | etot = -180.770700648445
+30000  ekin = 23.8432321400247 |  erot = 18.4812216983637 | epot = -223.095154486375 | etot = -180.770700647986
+31000  ekin = 23.9793041752229 |  erot = 18.330784533402 | epot = -223.08078935577 | etot = -180.770700647145
+32000  ekin = 24.0810246040235 |  erot = 18.2261577056003 | epot = -223.077882955919 | etot = -180.770700646295
+33000  ekin = 24.1468986449398 |  erot = 18.1820705445406 | epot = -223.09966983514 | etot = -180.770700645659
+34000  ekin = 24.1756615132863 |  erot = 18.2103812210172 | epot = -223.156743379607 | etot = -180.770700645303
+35000  ekin = 24.1663193894652 |  erot = 18.3185351073568 | epot = -223.255555142089 | etot = -180.770700645267
+36000  ekin = 24.1167205812964 |  erot = 18.5091649894187 | epot = -223.396586216223 | etot = -180.770700645508
+37000  ekin = 24.0274860006135 |  erot = 18.7785134320989 | epot = -223.576700078937 | etot = -180.770700646225
+38000  ekin = 23.8991479078985 |  erot = 19.1166063146995 | epot = -223.78645486989 | etot = -180.770700647292
+39000  ekin = 23.7326911853236 |  erot = 19.5069160952493 | epot = -224.010307929336 | etot = -180.770700648763
+40000  ekin = 23.5294223072121 |  erot = 19.9254673141826 | epot = -224.225590272292 | etot = -180.770700650897
+41000  ekin = 23.2899396141392 |  erot = 20.340809778056 | epot = -224.401450045567 | etot = -180.770700653371
+42000  ekin = 23.0154529235024 |  erot = 20.7165619564844 | epot = -224.502715535761 | etot = -180.770700655774
+43000  ekin = 22.7111536814278 |  erot = 21.0163895622227 | epot = -224.498243901357 | etot = -180.770700657707
+44000  ekin = 22.3710575806356 |  erot = 21.2060371289779 | epot = -224.347795365752 | etot = -180.770700656139
+45000  ekin = 22.0515843162889 |  erot = 21.2588026881767 | epot = -224.08108764689 | etot = -180.770700642424
+46000  ekin = 21.7855632553132 |  erot = 21.2036013766601 | epot = -223.75986526006 | etot = -180.770700628087
+47000  ekin = 21.5167766971454 |  erot = 21.0656367023669 | epot = -223.353114011014 | etot = -180.770700611502
+48000  ekin = 21.4540196107332 |  erot = 20.8430832424325 | epot = -223.067803499524 | etot = -180.770700646358
+49000  ekin = 21.3647564765273 |  erot = 20.5521507191689 | epot = -222.68760781692 | etot = -180.770700621224
+50000  ekin = 21.3125768184616 |  erot = 20.2526464671335 | epot = -222.335923904309 | etot = -180.770700618713
+51000  ekin = 21.2949924810833 |  erot = 19.9798421626046 | epot = -222.045535260403 | etot = -180.770700616715
+52000  ekin = 21.313714424968 |  erot = 19.762769134369 | epot = -221.847184173962 | etot = -180.770700614625
+53000  ekin = 21.3664076685101 |  erot = 19.6202359856903 | epot = -221.757344279694 | etot = -180.770700625493
+54000  ekin = 21.4214245524056 |  erot = 19.5588232319504 | epot = -221.750948393747 | etot = -180.770700609391
+55000  ekin = 21.5995673396088 |  erot = 19.5805214885682 | epot = -221.950789453583 | etot = -180.770700625406
+56000  ekin = 21.7643125668302 |  erot = 19.6816042107783 | epot = -222.216617401428 | etot = -180.77070062382
+57000  ekin = 21.922130908444 |  erot = 19.8499880475958 | epot = -222.542819582063 | etot = -180.770700626024
+58000  ekin = 22.0666093644387 |  erot = 20.0713856445721 | epot = -222.908695636277 | etot = -180.770700627266
+59000  ekin = 22.1910921687945 |  erot = 20.3284024096015 | epot = -223.290195207095 | etot = -180.770700628699
+60000  ekin = 22.2920682490233 |  erot = 20.6003319531545 | epot = -223.663100832376 | etot = -180.770700630198
+61000  ekin = 22.3680528265786 |  erot = 20.8645614198866 | epot = -224.003314878046 | etot = -180.77070063158
+62000  ekin = 22.4198570332631 |  erot = 21.0983714926633 | epot = -224.288929158679 | etot = -180.770700632752
+63000  ekin = 22.450080073992 |  erot = 21.28155214409 | epot = -224.502332851296 | etot = -180.770700633215
+64000  ekin = 22.4634052763983 |  erot = 21.3990470998282 | epot = -224.633153009903 | etot = -180.770700633676
+65000  ekin = 22.4639885390964 |  erot = 21.4413332838528 | epot = -224.676022456447 | etot = -180.770700633498
+66000  ekin = 22.4559522488544 |  erot = 21.4074154510867 | epot = -224.634068332758 | etot = -180.770700632817
+67000  ekin = 22.4417384097826 |  erot = 21.3051580893564 | epot = -224.517597130738 | etot = -180.770700631599
+68000  ekin = 22.421878544646 |  erot = 21.1490017805243 | epot = -224.34158095606 | etot = -180.77070063089
+69000  ekin = 22.3954651199576 |  erot = 20.9555571676358 | epot = -224.121722917263 | etot = -180.770700629669
+70000  ekin = 22.3613349801193 |  erot = 20.7433545871758 | epot = -223.875390195706 | etot = -180.770700628411
+71000  ekin = 22.3171019087139 |  erot = 20.5301141425049 | epot = -223.617916679045 | etot = -180.770700627826
+72000  ekin = 22.2595195485147 |  erot = 20.3296309382964 | epot = -223.359851114099 | etot = -180.770700627288
+73000  ekin = 22.1869461213877 |  erot = 20.1521902584588 | epot = -223.109837006429 | etot = -180.770700626583
+74000  ekin = 22.0990935565683 |  erot = 20.0059494138149 | epot = -222.875743596756 | etot = -180.770700626373
+75000  ekin = 21.9959491639282 |  erot = 19.8965902063256 | epot = -222.663239996049 | etot = -180.770700625795
+76000  ekin = 21.8806005890445 |  erot = 19.828424336326 | epot = -222.479725550679 | etot = -180.770700625308
+77000  ekin = 21.7590261899809 |  erot = 19.8043252195864 | epot = -222.334052034216 | etot = -180.770700624649
+78000  ekin = 21.6392419839503 |  erot = 19.8262630279236 | epot = -222.236205635986 | etot = -180.770700624113
+79000  ekin = 21.5302317519716 |  erot = 19.8938812521576 | epot = -222.194813627769 | etot = -180.77070062364
+80000  ekin = 21.4402276725657 |  erot = 20.0060100278943 | epot = -222.216938324074 | etot = -180.770700623614
+81000  ekin = 21.3741486759855 |  erot = 20.158514479161 | epot = -222.303363779439 | etot = -180.770700624292
+82000  ekin = 21.3325013763505 |  erot = 20.3431413542724 | epot = -222.44634335588 | etot = -180.770700625257
+83000  ekin = 21.3128808684037 |  erot = 20.548330990772 | epot = -222.631912485779 | etot = -180.770700626604
+84000  ekin = 21.310766170793 |  erot = 20.7607919785174 | epot = -222.842258777119 | etot = -180.770700627809
+85000  ekin = 21.3216301567277 |  erot = 20.9678418539246 | epot = -223.060172639485 | etot = -180.770700628833
+86000  ekin = 21.3400295156723 |  erot = 21.1566564817957 | epot = -223.267386627523 | etot = -180.770700630055
+87000  ekin = 21.3617783036992 |  erot = 21.3170902458394 | epot = -223.449569179882 | etot = -180.770700630344
+88000  ekin = 21.3873913218409 |  erot = 21.445443991042 | epot = -223.603535942848 | etot = -180.770700629965
+89000  ekin = 21.421574069399 |  erot = 21.5439953706456 | epot = -223.736270068948 | etot = -180.770700628904
+90000  ekin = 21.4723781618091 |  erot = 21.6216769093347 | epot = -223.86475569847 | etot = -180.770700627326
+91000  ekin = 21.549406625472 |  erot = 21.6927202486463 | epot = -224.012827499723 | etot = -180.770700625604
+92000  ekin = 21.6619209347597 |  erot = 21.7730744493012 | epot = -224.205696008348 | etot = -180.770700624287
+93000  ekin = 21.8158778641472 |  erot = 21.8756732628048 | epot = -224.462251750825 | etot = -180.770700623873
+94000  ekin = 22.0110275730997 |  erot = 22.0060799403022 | epot = -224.787808138196 | etot = -180.770700624794
+95000  ekin = 22.2387555838384 |  erot = 22.1596167137192 | epot = -225.16907292429 | etot = -180.770700626733
+96000  ekin = 22.4832444899361 |  erot = 22.3220202374401 | epot = -225.575965356875 | etot = -180.770700629499
+97000  ekin = 22.7237276202693 |  erot = 22.4720556690122 | epot = -225.966483921719 | etot = -180.770700632437
+98000  ekin = 22.9377647716041 |  erot = 22.5858660312277 | epot = -226.294331437118 | etot = -180.770700634287
+99000  ekin = 23.1071231637237 |  erot = 22.6457411046184 | epot = -226.523564904806 | etot = -180.770700636464
+100000  ekin = 23.2156001924311 |  erot = 22.6390310936006 | epot = -226.625331923822 | etot = -180.770700637791
+  100000   0.10528617   -1.5761124  0.044860201   -1.3743901 -1.9205819e-05      1000000 
+Loop time of 83.9672 on 1 procs for 100000 steps with 148 atoms
+
+Performance: 1028.974 tau/day, 1190.942 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 80.885     | 80.885     | 80.885     |   0.0 | 96.33
+Bond    | 0.94789    | 0.94789    | 0.94789    |   0.0 |  1.13
+Neigh   | 0.011589   | 0.011589   | 0.011589   |   0.0 |  0.01
+Comm    | 0.045979   | 0.045979   | 0.045979   |   0.0 |  0.05
+Output  | 0.11973    | 0.11973    | 0.11973    |   0.0 |  0.14
+Modify  | 1.8641     | 1.8641     | 1.8641     |   0.0 |  2.22
+Other   |            | 0.09239    |            |       |  0.11
+
+Nlocal:        148.000 ave         148 max         148 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:         0.00000 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:        4199.00 ave        4199 max        4199 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 4199
+Ave neighs/atom = 28.371622
+Ave special neighs/atom = 6.0000000
+Neighbor list builds = 100
+Dangerous builds = 0
+
+write_data last_config.${number}.* nocoeff
+write_data last_config.5.* nocoeff
+System init for write_data ...
+#write_restart last_config.${number}.*
+Total wall time: 0:01:23

examples/PACKAGES/cgdna/examples/oxDNA2/dsring/log.2Jul21.dsring.g++.4

@@ -0,0 +1,281 @@
+LAMMPS (2 Jul 2021)
+variable number	equal 5
+variable ofreq	equal 1000
+variable efreq	equal 1000
+variable T      equal 0.1
+variable rhos   equal 0.2
+
+units lj
+
+dimension 3
+
+newton on
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid oxdna
+WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:157)
+atom_modify sort 0 1.0
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 2.0 bin
+neigh_modify every 1 delay 0 check yes
+
+read_data data.dsring
+Reading data file ...
+  orthogonal box = (0.0000000 0.0000000 0.0000000) to (100.00000 100.00000 100.00000)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  148 atoms
+  reading velocities ...
+  148 velocities
+  scanning bonds ...
+  1 = max bonds/atom
+  148 ellipsoids
+  reading bonds ...
+  148 bonds
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     2 = max # of 1-2 neighbors
+     2 = max # of 1-3 neighbors
+     4 = max # of 1-4 neighbors
+     6 = max # of special neighbors
+  special bonds CPU = 0.001 seconds
+  read_data CPU = 0.008 seconds
+
+set atom * mass 3.1575
+Setting atom values ...
+  148 settings made for mass
+
+group all type 1 4
+148 atoms in group all
+
+# oxDNA2 bond interactions - FENE backbone
+bond_style oxdna2/fene
+bond_coeff * 2.0 0.25 0.7564
+special_bonds lj 0 1 1
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        1        1       
+  special bond factors coul:  0        0        0       
+     2 = max # of 1-2 neighbors
+     2 = max # of 1-3 neighbors
+     4 = max # of 1-4 neighbors
+     6 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
+
+# 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 0.75 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
+pair_coeff * * oxdna2/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
+pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
+pair_coeff * * oxdna2/dh      ${T} ${rhos} 0.815
+pair_coeff * * oxdna2/dh      0.1 ${rhos} 0.815
+pair_coeff * * oxdna2/dh      0.1 0.2 0.815
+
+# NVE ensemble
+fix 1 all nve/asphere
+#fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10
+
+timestep 1e-5
+
+#comm_style tiled
+fix 3 all balance 1000 1.03 shift xyz 10 1.03
+comm_modify cutoff 3.8
+
+compute quat all property/atom quatw quati quatj quatk
+
+compute erot all erotate/asphere
+compute ekin all ke
+compute epot all pe
+variable erot equal c_erot
+variable ekin equal c_ekin
+variable epot equal c_epot
+variable etot equal c_erot+c_ekin+c_epot
+fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+fix 5 all print 1000 "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+
+dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
+dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
+dump out all custom 1000 out.5.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
+dump_modify out sort id
+dump_modify out format line "%d %d %d  %22.15le %22.15le %22.15le  %d %d %d  %22.15le %22.15le %22.15le  %22.15le %22.15le %22.15le %22.15le  %22.15le %22.15le %22.15le"
+
+run 100000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.6389877
+  ghost atom cutoff = 5.6389877
+  binsize = 2.8194939, bins = 36 36 36
+  5 neighbor lists, perpetual/occasional/extra = 5 0 0
+  (1) pair oxdna2/excv, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+  (2) pair oxdna2/hbond, perpetual, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (3) pair oxdna2/xstk, perpetual, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (4) pair oxdna2/coaxstk, perpetual, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (5) pair oxdna2/dh, perpetual, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+WARNING: Communication cutoff adjusted to 5.638987723814632 (../comm.cpp:739)
+0  ekin = 20.4724634226502 |  erot = 21.0406985312466 | epot = -222.283862600785 | etot = -180.770700646889
+Per MPI rank memory allocation (min/avg/max) = 9.383 | 9.432 | 9.506 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume 
+       0  0.092845639   -1.5501211   0.04820308   -1.3635905 -9.0052368e-06      1000000 
+1000  ekin = 20.531989141805 |  erot = 21.2158633183735 | epot = -222.518553109361 | etot = -180.770700649183
+2000  ekin = 20.585620972069 |  erot = 21.391859435226 | epot = -222.748181058335 | etot = -180.77070065104
+3000  ekin = 20.6239332104643 |  erot = 21.5529389082727 | epot = -222.947572771312 | etot = -180.770700652575
+4000  ekin = 20.6395549184482 |  erot = 21.6854113323894 | epot = -223.095666904229 | etot = -180.770700653391
+5000  ekin = 20.6295551742564 |  erot = 21.7809539301804 | epot = -223.181209757876 | etot = -180.770700653439
+6000  ekin = 20.5959625511847 |  erot = 21.8369756530726 | epot = -223.203638857302 | etot = -180.770700653045
+7000  ekin = 20.5431034482069 |  erot = 21.8556844173874 | epot = -223.169488517717 | etot = -180.770700652123
+8000  ekin = 20.4774701419093 |  erot = 21.8437134145373 | epot = -223.09188420739 | etot = -180.770700650943
+9000  ekin = 20.4074566554239 |  erot = 21.8097283692397 | epot = -222.987885674261 | etot = -180.770700649598
+10000  ekin = 20.3427303660297 |  erot = 21.7629575866662 | epot = -222.876388600949 | etot = -180.770700648253
+11000  ekin = 20.2927407149578 |  erot = 21.7112100845349 | epot = -222.774651446682 | etot = -180.77070064719
+12000  ekin = 20.2665977502213 |  erot = 21.6594999867139 | epot = -222.696798383222 | etot = -180.770700646287
+13000  ekin = 20.2733920359447 |  erot = 21.6092715397933 | epot = -222.653364221617 | etot = -180.770700645879
+14000  ekin = 20.3196524789069 |  erot = 21.5586630974992 | epot = -222.649016222076 | etot = -180.77070064567
+15000  ekin = 20.410400937429 |  erot = 21.5031572556307 | epot = -222.684258838858 | etot = -180.770700645799
+16000  ekin = 20.5472869005792 |  erot = 21.4346177247041 | epot = -222.752605272037 | etot = -180.770700646753
+17000  ekin = 20.7266657908773 |  erot = 21.3426631585218 | epot = -222.840029597232 | etot = -180.770700647833
+18000  ekin = 20.9417612759978 |  erot = 21.2178611180927 | epot = -222.930323042998 | etot = -180.770700648907
+19000  ekin = 21.1819308659396 |  erot = 21.0532289630294 | epot = -223.005860478921 | etot = -180.770700649952
+20000  ekin = 21.4358169889472 |  erot = 20.8473069564707 | epot = -223.053824595387 | etot = -180.77070064997
+21000  ekin = 21.6968513750995 |  erot = 20.6066744652585 | epot = -223.074226489837 | etot = -180.770700649479
+22000  ekin = 21.9614458442779 |  erot = 20.3429420444508 | epot = -223.075088537371 | etot = -180.770700648642
+23000  ekin = 22.2276099755697 |  erot = 20.070338516524 | epot = -223.068649139875 | etot = -180.770700647781
+24000  ekin = 22.4935893196667 |  erot = 19.8020671721661 | epot = -223.066357139277 | etot = -180.770700647444
+25000  ekin = 22.756606454822 |  erot = 19.5464828008836 | epot = -223.073789902976 | etot = -180.77070064727
+26000  ekin = 23.0126717548391 |  erot = 19.3065017718461 | epot = -223.089874174572 | etot = -180.770700647887
+27000  ekin = 23.2550417060586 |  erot = 19.0797753474566 | epot = -223.105517701932 | etot = -180.770700648417
+28000  ekin = 23.4774329734797 |  erot = 18.8646197299572 | epot = -223.112753352067 | etot = -180.77070064863
+29000  ekin = 23.6747927720654 |  erot = 18.6628653411822 | epot = -223.108358761694 | etot = -180.770700648446
+30000  ekin = 23.8432321400238 |  erot = 18.4812216983633 | epot = -223.095154486375 | etot = -180.770700647988
+31000  ekin = 23.979304175222 |  erot = 18.3307845334015 | epot = -223.08078935577 | etot = -180.770700647146
+32000  ekin = 24.0810246040226 |  erot = 18.2261577055998 | epot = -223.077882955919 | etot = -180.770700646297
+33000  ekin = 24.1468986449389 |  erot = 18.1820705445401 | epot = -223.09966983514 | etot = -180.770700645661
+34000  ekin = 24.1756615132855 |  erot = 18.2103812210167 | epot = -223.156743379607 | etot = -180.770700645304
+35000  ekin = 24.1663193894644 |  erot = 18.3185351073563 | epot = -223.255555142089 | etot = -180.770700645269
+36000  ekin = 24.1167205812957 |  erot = 18.5091649894184 | epot = -223.396586216223 | etot = -180.770700645509
+37000  ekin = 24.0274860006128 |  erot = 18.7785134320987 | epot = -223.576700078937 | etot = -180.770700646226
+38000  ekin = 23.8991479078978 |  erot = 19.1166063146994 | epot = -223.786454869891 | etot = -180.770700647293
+39000  ekin = 23.7326911853231 |  erot = 19.5069160952493 | epot = -224.010307929336 | etot = -180.770700648764
+40000  ekin = 23.5294223072117 |  erot = 19.9254673141828 | epot = -224.225590272293 | etot = -180.770700650899
+41000  ekin = 23.289939614139 |  erot = 20.3408097780563 | epot = -224.401450045568 | etot = -180.770700653372
+42000  ekin = 23.0154529235022 |  erot = 20.7165619564848 | epot = -224.502715535762 | etot = -180.770700655775
+43000  ekin = 22.7111536814277 |  erot = 21.0163895622231 | epot = -224.498243901359 | etot = -180.770700657708
+44000  ekin = 22.3710575806355 |  erot = 21.2060371289783 | epot = -224.347795365754 | etot = -180.77070065614
+45000  ekin = 22.0515843162889 |  erot = 21.2588026881768 | epot = -224.081087646891 | etot = -180.770700642425
+46000  ekin = 21.7855632553133 |  erot = 21.20360137666 | epot = -223.759865260062 | etot = -180.770700628089
+47000  ekin = 21.5167766971456 |  erot = 21.0656367023667 | epot = -223.353114011016 | etot = -180.770700611503
+48000  ekin = 21.4540196107333 |  erot = 20.8430832424321 | epot = -223.067803499525 | etot = -180.77070064636
+49000  ekin = 21.3647564765274 |  erot = 20.5521507191682 | epot = -222.687607816922 | etot = -180.770700621226
+50000  ekin = 21.3125768184617 |  erot = 20.2526464671325 | epot = -222.33592390431 | etot = -180.770700618715
+51000  ekin = 21.2949924810834 |  erot = 19.9798421626035 | epot = -222.045535260404 | etot = -180.770700616717
+52000  ekin = 21.3137144249679 |  erot = 19.7627691343679 | epot = -221.847184173963 | etot = -180.770700614627
+53000  ekin = 21.3664076685099 |  erot = 19.6202359856891 | epot = -221.757344279695 | etot = -180.770700625496
+54000  ekin = 21.4214245524052 |  erot = 19.5588232319492 | epot = -221.750948393748 | etot = -180.770700609393
+55000  ekin = 21.5995673396082 |  erot = 19.580521488567 | epot = -221.950789453583 | etot = -180.770700625408
+56000  ekin = 21.7643125668294 |  erot = 19.681604210777 | epot = -222.216617401429 | etot = -180.770700623823
+57000  ekin = 21.922130908443 |  erot = 19.8499880475945 | epot = -222.542819582064 | etot = -180.770700626026
+58000  ekin = 22.0666093644375 |  erot = 20.0713856445709 | epot = -222.908695636278 | etot = -180.770700627269
+59000  ekin = 22.1910921687932 |  erot = 20.3284024096003 | epot = -223.290195207095 | etot = -180.770700628702
+60000  ekin = 22.2920682490219 |  erot = 20.6003319531534 | epot = -223.663100832376 | etot = -180.770700630201
+61000  ekin = 22.3680528265772 |  erot = 20.8645614198856 | epot = -224.003314878046 | etot = -180.770700631583
+62000  ekin = 22.4198570332617 |  erot = 21.0983714926625 | epot = -224.288929158679 | etot = -180.770700632755
+63000  ekin = 22.4500800739905 |  erot = 21.2815521440892 | epot = -224.502332851297 | etot = -180.770700633217
+64000  ekin = 22.4634052763968 |  erot = 21.3990470998276 | epot = -224.633153009904 | etot = -180.770700633679
+65000  ekin = 22.463988539095 |  erot = 21.4413332838523 | epot = -224.676022456448 | etot = -180.770700633501
+66000  ekin = 22.4559522488531 |  erot = 21.4074154510864 | epot = -224.634068332759 | etot = -180.770700632819
+67000  ekin = 22.4417384097814 |  erot = 21.3051580893563 | epot = -224.517597130739 | etot = -180.770700631601
+68000  ekin = 22.4218785446449 |  erot = 21.1490017805243 | epot = -224.341580956061 | etot = -180.770700630892
+69000  ekin = 22.3954651199567 |  erot = 20.9555571676359 | epot = -224.121722917264 | etot = -180.770700629671
+70000  ekin = 22.3613349801186 |  erot = 20.743354587176 | epot = -223.875390195707 | etot = -180.770700628413
+71000  ekin = 22.3171019087134 |  erot = 20.5301141425052 | epot = -223.617916679047 | etot = -180.770700627829
+72000  ekin = 22.2595195485144 |  erot = 20.3296309382966 | epot = -223.3598511141 | etot = -180.77070062729
+73000  ekin = 22.1869461213875 |  erot = 20.1521902584591 | epot = -223.109837006431 | etot = -180.770700626585
+74000  ekin = 22.0990935565682 |  erot = 20.0059494138151 | epot = -222.875743596758 | etot = -180.770700626375
+75000  ekin = 21.9959491639282 |  erot = 19.8965902063257 | epot = -222.663239996051 | etot = -180.770700625797
+76000  ekin = 21.8806005890446 |  erot = 19.8284243363261 | epot = -222.479725550681 | etot = -180.77070062531
+77000  ekin = 21.759026189981 |  erot = 19.8043252195865 | epot = -222.334052034218 | etot = -180.770700624651
+78000  ekin = 21.6392419839505 |  erot = 19.8262630279235 | epot = -222.236205635988 | etot = -180.770700624114
+79000  ekin = 21.5302317519718 |  erot = 19.8938812521574 | epot = -222.19481362777 | etot = -180.770700623641
+80000  ekin = 21.4402276725659 |  erot = 20.0060100278939 | epot = -222.216938324075 | etot = -180.770700623615
+81000  ekin = 21.3741486759857 |  erot = 20.1585144791605 | epot = -222.303363779439 | etot = -180.770700624293
+82000  ekin = 21.3325013763506 |  erot = 20.3431413542717 | epot = -222.446343355881 | etot = -180.770700625259
+83000  ekin = 21.3128808684039 |  erot = 20.5483309907712 | epot = -222.63191248578 | etot = -180.770700626605
+84000  ekin = 21.3107661707932 |  erot = 20.7607919785166 | epot = -222.842258777119 | etot = -180.77070062781
+85000  ekin = 21.3216301567279 |  erot = 20.9678418539237 | epot = -223.060172639486 | etot = -180.770700628834
+86000  ekin = 21.3400295156725 |  erot = 21.1566564817949 | epot = -223.267386627524 | etot = -180.770700630057
+87000  ekin = 21.3617783036995 |  erot = 21.3170902458388 | epot = -223.449569179883 | etot = -180.770700630345
+88000  ekin = 21.3873913218413 |  erot = 21.4454439910414 | epot = -223.603535942849 | etot = -180.770700629967
+89000  ekin = 21.4215740693994 |  erot = 21.5439953706451 | epot = -223.73627006895 | etot = -180.770700628906
+90000  ekin = 21.4723781618096 |  erot = 21.6216769093343 | epot = -223.864755698472 | etot = -180.770700627328
+91000  ekin = 21.5494066254725 |  erot = 21.6927202486459 | epot = -224.012827499725 | etot = -180.770700625606
+92000  ekin = 21.6619209347601 |  erot = 21.7730744493007 | epot = -224.20569600835 | etot = -180.77070062429
+93000  ekin = 21.8158778641474 |  erot = 21.8756732628043 | epot = -224.462251750827 | etot = -180.770700623875
+94000  ekin = 22.0110275730999 |  erot = 22.0060799403016 | epot = -224.787808138198 | etot = -180.770700624796
+95000  ekin = 22.2387555838384 |  erot = 22.1596167137185 | epot = -225.169072924291 | etot = -180.770700626735
+96000  ekin = 22.4832444899359 |  erot = 22.3220202374394 | epot = -225.575965356876 | etot = -180.770700629501
+97000  ekin = 22.7237276202691 |  erot = 22.4720556690115 | epot = -225.966483921719 | etot = -180.770700632439
+98000  ekin = 22.9377647716038 |  erot = 22.5858660312271 | epot = -226.294331437119 | etot = -180.770700634288
+99000  ekin = 23.1071231637233 |  erot = 22.645741104618 | epot = -226.523564904806 | etot = -180.770700636465
+100000  ekin = 23.2156001924307 |  erot = 22.6390310936004 | epot = -226.625331923823 | etot = -180.770700637791
+  100000   0.10528617   -1.5761124  0.044860201   -1.3743901 -1.9205819e-05      1000000 
+Loop time of 28.0802 on 4 procs for 100000 steps with 148 atoms
+
+Performance: 3076.899 tau/day, 3561.226 timesteps/s
+99.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 16.209     | 21.356     | 25.248     |  81.3 | 76.05
+Bond    | 0.26072    | 0.26526    | 0.27015    |   0.9 |  0.94
+Neigh   | 0.005772   | 0.0058625  | 0.005932   |   0.1 |  0.02
+Comm    | 1.7227     | 5.6246     | 10.79      | 158.9 | 20.03
+Output  | 0.043943   | 0.046855   | 0.048664   |   0.9 |  0.17
+Modify  | 0.54715    | 0.55336    | 0.55902    |   0.7 |  1.97
+Other   |            | 0.2279     |            |       |  0.81
+
+Nlocal:        37.0000 ave          38 max          36 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Nghost:        111.000 ave         112 max         110 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Neighs:        1049.75 ave        1270 max         757 min
+Histogram: 1 0 0 1 0 0 0 0 0 2
+
+Total # of neighbors = 4199
+Ave neighs/atom = 28.371622
+Ave special neighs/atom = 6.0000000
+Neighbor list builds = 100
+Dangerous builds = 0
+
+write_data last_config.${number}.* nocoeff
+write_data last_config.5.* nocoeff
+System init for write_data ...
+#write_restart last_config.${number}.*
+Total wall time: 0:00:28

examples/PACKAGES/cgdna/examples/oxDNA2/duplex1/in.duplex1

@@ -8,7 +8,7 @@ units lj
 
 dimension 3
 
-newton off
+newton on
 
 boundary  p p p
 
@@ -69,3 +69,4 @@ dump_modify out format line "%d %d %d  %22.15le %22.15le %22.15le  %d %d %d  %22
 run 1000000
 
 write_data last_config.${number}.* nocoeff
+#write_restart last_config.${number}.*

examples/PACKAGES/cgdna/examples/oxDNA2/duplex2/in.duplex2

@@ -8,7 +8,7 @@ units lj
 
 dimension 3
 
-newton off
+newton on
 
 boundary  p p p
 
@@ -69,3 +69,4 @@ dump_modify out format line "%d %d %d  %22.15le %22.15le %22.15le  %d %d %d  %22
 run 1000000
 
 write_data last_config.${number}.* nocoeff
+#write_restart last_config.${number}.*

examples/PACKAGES/cgdna/examples/oxDNA2/duplex3/in.duplex3

@@ -8,7 +8,7 @@ units lj
 
 dimension 3
 
-newton off
+newton on
 
 boundary  p p p
 
@@ -69,3 +69,4 @@ dump_modify out format line "%d %d %d  %22.15le %22.15le %22.15le  %d %d %d  %22
 run 1000000
 
 write_data last_config.${number}.* nocoeff
+#write_restart last_config.${number}.*

examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/in.duplex4.4type

@@ -11,7 +11,7 @@ units lj
 
 dimension 3
 
-newton off
+newton on
 
 boundary  p p p
 
@@ -84,3 +84,4 @@ dump_modify out format line "%d %d %d  %22.15le %22.15le %22.15le  %d %d %d  %22
 run 1000000
 
 write_data last_config.${number}.* nocoeff
+#write_restart last_config.${number}.*

examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/in.duplex4.8type

@@ -11,7 +11,7 @@ units lj
 
 dimension 3
 
-newton off
+newton on
 
 boundary  p p p
 
@@ -84,3 +84,4 @@ dump_modify out format line "%d %d %d  %22.15le %22.15le %22.15le  %d %d %d  %22
 run 1000000
 
 write_data last_config.${number}.* nocoeff
+#write_restart last_config.${number}.*

examples/PACKAGES/cgdna/examples/oxRNA2/duplex2/in.duplex2

@@ -8,7 +8,7 @@ units lj
 
 dimension 3
 
-newton off
+newton on
 
 boundary  p p p
 
@@ -70,3 +70,4 @@ dump_modify out format line "%d %d %d  %22.15le %22.15le %22.15le  %d %d %d  %22
 run 1000000
 
 write_data last_config.${number}.* nocoeff
+#write_restart last_config.${number}.*

examples/PACKAGES/cgdna/examples/test.sh

@@ -0,0 +1,232 @@
+#! /bin/bash
+
+DATE='2Jul21'
+LMPDIR=/Users/ohenrich/Work/code/lammps
+
+SRCDIR=$LMPDIR/src
+EXDIR=$LMPDIR/examples/PACKAGES/cgdna/examples
+
+if [ $# -eq 1 ] && [ $1 = run ]; then
+  echo '# Compiling executable in' $SRCDIR
+
+  cd $SRCDIR
+  make clean-all
+  make -j8 mpi
+
+  ######################################################
+  echo '# Running oxDNA duplex1 test'
+  cd $EXDIR/oxDNA/duplex1
+  mkdir test
+  cd test
+  cp $SRCDIR/lmp_mpi .
+  cp ../in.duplex1 .
+  cp ../data.duplex1 .
+
+  mpirun -np 1 ./lmp_mpi < in.duplex1 > /dev/null
+  mv log.lammps log.$DATE.duplex1.g++.1
+  grep etot log.$DATE.duplex1.g++.1 > e_test.dat
+  grep etot ../log*1 > e_old.dat
+  ndiff -relerr 1e-8 e_test.dat e_old.dat
+
+  mpirun -np 4 ./lmp_mpi < in.duplex1 > /dev/null
+  mv log.lammps log.$DATE.duplex1.g++.4
+  grep etot log.$DATE.duplex1.g++.4 > e_test.dat
+  grep etot ../log*4 > e_old.dat
+  ndiff -relerr 1e-8 e_test.dat e_old.dat
+
+  ######################################################
+
+  ######################################################
+  echo '# Running oxDNA duplex2 test'
+  cd $EXDIR/oxDNA/duplex2
+  mkdir test
+  cd test
+  cp $SRCDIR/lmp_mpi .
+  cp ../in.duplex2 .
+  cp ../data.duplex2 .
+
+  mpirun -np 1 ./lmp_mpi < in.duplex2 > /dev/null
+  mv log.lammps log.$DATE.duplex2.g++.1
+  grep etot log.$DATE.duplex2.g++.1 > e_test.dat
+  grep etot ../log*1 > e_old.dat
+  ndiff -relerr 1e-8 e_test.dat e_old.dat
+
+  mpirun -np 4 ./lmp_mpi < in.duplex2 > /dev/null
+  mv log.lammps log.$DATE.duplex2.g++.4
+  grep etot log.$DATE.duplex2.g++.4 > e_test.dat
+  grep etot ../log*4 > e_old.dat
+  ndiff -relerr 1e-8 e_test.dat e_old.dat
+
+  ######################################################
+
+  ######################################################
+  echo '# Running oxDNA2 duplex1 test'
+  cd $EXDIR/oxDNA2/duplex1
+  mkdir test
+  cd test
+  cp $SRCDIR/lmp_mpi .
+  cp ../in.duplex1 .
+  cp ../data.duplex1 .
+
+  mpirun -np 1 ./lmp_mpi < in.duplex1 > /dev/null
+  mv log.lammps log.$DATE.duplex1.g++.1
+  grep etot log.$DATE.duplex1.g++.1 > e_test.dat
+  grep etot ../log*1 > e_old.dat
+  ndiff -relerr 1e-8 e_test.dat e_old.dat
+
+  mpirun -np 4 ./lmp_mpi < in.duplex1 > /dev/null
+  mv log.lammps log.$DATE.duplex1.g++.4
+  grep etot log.$DATE.duplex1.g++.4 > e_test.dat
+  grep etot ../log*4 > e_old.dat
+  ndiff -relerr 1e-8 e_test.dat e_old.dat
+
+  ######################################################
+
+  ######################################################
+  echo '# Running oxDNA2 duplex2 test'
+  cd $EXDIR/oxDNA2/duplex2
+  mkdir test
+  cd test
+  cp $SRCDIR/lmp_mpi .
+  cp ../in.duplex2 .
+  cp ../data.duplex2 .
+
+  mpirun -np 1 ./lmp_mpi < in.duplex2 > /dev/null
+  mv log.lammps log.$DATE.duplex2.g++.1
+  grep etot log.$DATE.duplex2.g++.1 > e_test.dat
+  grep etot ../log*1 > e_old.dat
+  ndiff -relerr 1e-8 e_test.dat e_old.dat
+
+  mpirun -np 4 ./lmp_mpi < in.duplex2 > /dev/null
+  mv log.lammps log.$DATE.duplex2.g++.4
+  grep etot log.$DATE.duplex2.g++.4 > e_test.dat
+  grep etot ../log*4 > e_old.dat
+  ndiff -relerr 1e-8 e_test.dat e_old.dat
+
+  ######################################################
+
+  ######################################################
+  echo '# Running oxDNA2 duplex3 test'
+  cd $EXDIR/oxDNA2/duplex3
+  mkdir test
+  cd test
+  cp $SRCDIR/lmp_mpi .
+  cp ../in.duplex3 .
+  cp ../data.duplex3 .
+
+  mpirun -np 1 ./lmp_mpi < in.duplex3 > /dev/null
+  mv log.lammps log.$DATE.duplex3.g++.1
+  grep etot log.$DATE.duplex3.g++.1 > e_test.dat
+  grep etot ../log*1 > e_old.dat
+  ndiff -relerr 1e-8 e_test.dat e_old.dat
+
+  mpirun -np 4 ./lmp_mpi < in.duplex3 > /dev/null
+  mv log.lammps log.$DATE.duplex3.g++.4
+  grep etot  log.$DATE.duplex3.g++.4 > e_test.dat
+  grep etot ../log*4 > e_old.dat
+  ndiff -relerr 1e-8 e_test.dat e_old.dat
+
+  ######################################################
+
+  ######################################################
+  echo '# Running oxDNA2 unique_bp test'
+  cd $EXDIR/oxDNA2/unique_bp
+  mkdir test
+  cd test
+  cp $SRCDIR/lmp_mpi .
+  cp ../in.duplex4.4type .
+  cp ../in.duplex4.8type .
+  cp ../data.duplex4.4type .
+  cp ../data.duplex4.8type .
+
+  mpirun -np 1 ./lmp_mpi < in.duplex4.4type > /dev/null
+  mv log.lammps log.$DATE.duplex4.4type.g++.1
+  grep etot log.$DATE.duplex4.4type.g++.1 > e_test.dat
+  grep etot ../log*4type*1 > e_old.dat
+  ndiff -relerr 1e-8 e_test.dat e_old.dat
+
+  mpirun -np 4 ./lmp_mpi < in.duplex4.4type > /dev/null
+  mv log.lammps log.$DATE.duplex4.4type.g++.4
+  grep etot log.$DATE.duplex4.4type.g++.4 > e_test.dat
+  grep etot ../log*4type*4 > e_old.dat
+  ndiff -relerr 1e-8 e_test.dat e_old.dat
+
+  mpirun -np 1 ./lmp_mpi < in.duplex4.8type > /dev/null
+  mv log.lammps log.$DATE.duplex4.8type.g++.1
+  grep etot log.$DATE.duplex4.8type.g++.1 > e_test.dat
+  grep etot ../log*8type*1 > e_old.dat
+  ndiff -relerr 1e-8 e_test.dat e_old.dat
+
+  mpirun -np 4 ./lmp_mpi < in.duplex4.8type > /dev/null
+  mv log.lammps log.$DATE.duplex4.8type.g++.4
+  grep etot log.$DATE.duplex4.8type.g++.4 > e_test.dat
+  grep etot ../log*8type*4 > e_old.dat
+  ndiff -relerr 1e-8 e_test.dat e_old.dat
+
+  ######################################################
+
+  ######################################################
+  echo '# Running oxDNA2 dsring test'
+  cd $EXDIR/oxDNA2/dsring
+  mkdir test
+  cd test
+  cp $SRCDIR/lmp_mpi .
+  cp ../in.dsring .
+  cp ../data.dsring .
+
+  mpirun -np 1 ./lmp_mpi < in.dsring > /dev/null
+  mv log.lammps log.$DATE.dsring.g++.1
+  grep etot log.$DATE.dsring.g++.1 > e_test.dat
+  grep etot ../log*1 > e_old.dat
+  ndiff -relerr 1e-8 e_test.dat e_old.dat
+
+  mpirun -np 4 ./lmp_mpi < in.dsring > /dev/null
+  mv log.lammps log.$DATE.dsring.g++.4
+  grep etot log.$DATE.dsring.g++.4 > e_test.dat
+  grep etot ../log*4 > e_old.dat
+  ndiff -relerr 1e-8 e_test.dat e_old.dat
+
+  ######################################################
+
+  ######################################################
+  echo '# Running oxRNA2 duplex2 test'
+  cd $EXDIR/oxRNA2/duplex2
+  mkdir test
+  cd test
+  cp $SRCDIR/lmp_mpi .
+  cp ../in.duplex2 .
+  cp ../data.duplex2 .
+
+  mpirun -np 1 ./lmp_mpi < in.duplex2 > /dev/null
+  mv log.lammps log.$DATE.duplex2.g++.1
+  grep etot log.$DATE.duplex2.g++.1 > e_test.dat
+  grep etot ../log*1 > e_old.dat
+  ndiff -relerr 1e-8 e_test.dat e_old.dat
+
+  mpirun -np 4 ./lmp_mpi < in.duplex2 > /dev/null
+  mv log.lammps log.$DATE.duplex2.g++.4
+  grep etot log.$DATE.duplex2.g++.4 > e_test.dat
+  grep etot ../log*4 > e_old.dat
+  ndiff -relerr 1e-8 e_test.dat e_old.dat
+
+  ######################################################
+  echo '# Done'
+
+elif [ $# -eq 1 ] && [ $1 = clean ]; then
+  echo '# Deleting test directories'
+  rm -rf $EXDIR/oxDNA/duplex1/test
+  rm -rf $EXDIR/oxDNA/duplex2/test
+  rm -rf $EXDIR/oxDNA2/duplex1/test
+  rm -rf $EXDIR/oxDNA2/duplex2/test
+  rm -rf $EXDIR/oxDNA2/duplex3/test
+  rm -rf $EXDIR/oxDNA2/unique_bp/test
+  rm -rf $EXDIR/oxDNA2/dsring/test
+  rm -rf $EXDIR/oxRNA2/duplex2/test
+  echo '# Done'
+
+else
+  echo '# Usage:'
+  echo '# ./test.sh run  ... to run test suite'
+  echo '# ./test.sh clean ... to delete test directories'
+
+fi

src/CG-DNA/atom_vec_oxdna.cpp

@@ -15,6 +15,8 @@
 
 #include "atom.h"
 #include "comm.h"
+#include "error.h"
+#include "force.h"
 
 using namespace LAMMPS_NS;
 
@@ -46,6 +48,8 @@ AtomVecOxdna::AtomVecOxdna(LAMMPS *lmp) : AtomVec(lmp)
   fields_data_vel = (char *) "id v";
 
   setup_fields();
+
+  if(!force->newton_bond) error->warning(FLERR,"Write_data command requires newton on to preserve 3'->5' bond polarity");
 }
 
 /* ---------------------------------------------------------------------- */

src/CG-DNA/pair_oxdna2_excv.h

@@ -28,7 +28,6 @@ class PairOxdna2Excv : public PairOxdnaExcv {
  public:
   PairOxdna2Excv(class LAMMPS *lmp) : PairOxdnaExcv(lmp) {}
   virtual ~PairOxdna2Excv() {}
-
   virtual void compute_interaction_sites(double *, double *, double *, double *, double *);
 };
 

src/CG-DNA/pair_oxrna2_dh.h

@@ -26,7 +26,7 @@ namespace LAMMPS_NS {
 
 class PairOxrna2Dh : public PairOxdna2Dh {
  public:
-  PairOxrna2Dh(class LAMMPS *) : PairOxdna2Dh(lmp) {}
+  PairOxrna2Dh(class LAMMPS *lmp) : PairOxdna2Dh(lmp) {}
   virtual ~PairOxrna2Dh() {}
   virtual void compute_interaction_sites(double *, double *, double *, double *);
 };

src/CG-DNA/pair_oxrna2_excv.h

@@ -26,7 +26,7 @@ namespace LAMMPS_NS {
 
 class PairOxrna2Excv : public PairOxdnaExcv {
  public:
-  PairOxrna2Excv(class LAMMPS *) : PairOxdnaExcv(lmp) {}
+  PairOxrna2Excv(class LAMMPS *lmp) : PairOxdnaExcv(lmp) {}
   virtual ~PairOxrna2Excv() {}
   virtual void compute_interaction_sites(double *, double *, double *, double *, double *);
 };