Merge branch 'develop' into electrode

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

@@ -0,0 +1,70 @@
+variable number	equal 1
+variable ofreq	equal 1000
+variable efreq	equal 1000
+variable T      equal 0.1
+
+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.duplex1
+
+set atom * mass 3.1575
+
+group all type 1 4
+
+# oxDNA bond interactions - FENE backbone
+bond_style oxdna/fene
+bond_coeff * oxdna_lj.cgdna
+special_bonds lj 0 1 1
+
+# oxDNA pair interactions
+pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
+pair_coeff * * oxdna/excv    oxdna_lj.cgdna
+pair_coeff * * oxdna/stk     seqav 0.1 1.3448 2.6568 oxdna_lj.cgdna
+pair_coeff * * oxdna/hbond   seqav oxdna_lj.cgdna
+pair_coeff 1 4 oxdna/hbond   seqav oxdna_lj.cgdna
+pair_coeff 2 3 oxdna/hbond   seqav oxdna_lj.cgdna
+pair_coeff * * oxdna/xstk    oxdna_lj.cgdna
+pair_coeff * * oxdna/coaxstk oxdna_lj.cgdna
+
+# 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 1000000
+
+write_data last_config.${number}.* nocoeff
+#write_restart last_config.${number}.*

examples/PACKAGES/cgdna/examples/lj_units/oxDNA/potential_file/oxdna_lj.cgdna

@@ -0,0 +1 @@
+../../../../../../../potentials/oxdna_lj.cgdna

examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/duplex1/data.duplex1

@@ -0,0 +1,68 @@
+LAMMPS data file via write_data, version 27 May 2021
+
+10 atoms
+4 atom types
+8 bonds
+1 bond types
+10 ellipsoids
+
+-20 20 xlo xhi
+-20 20 ylo yhi
+-20 20 zlo zhi
+
+Masses
+
+1 3.1575
+2 3.1575
+3 3.1575
+4 3.1575
+
+Atoms # hybrid
+
+1 1 -0.33741452300167507 -0.43708835412476305 0.6450685042019271 1 1 3.7269849963023267 0 0 0
+2 2 -0.32142606102826937 -0.7137743037592722 1.1817366147004618 1 1 3.7269849963023267 0 0 0
+3 3 -0.130363628207774 -0.9147144801536078 1.62581312195109 1 1 3.7269849963023267 0 0 0
+4 4 0.16795127962282844 -0.9808507459807022 2.0894908590909003 1 1 3.7269849963023267 0 0 0
+5 1 0.46370423490634166 -0.7803347954883079 2.4251986815515827 1 1 3.7269849963023267 0 0 0
+6 4 -0.4462950185476711 0.09062163051035639 2.4668941268777607 2 1 3.7269849963023267 0 0 0
+7 1 -0.03377054097560965 0.20979847489755046 2.078208732038921 2 1 3.7269849963023267 0 0 0
+8 2 0.3297325391466579 0.17657587120899895 1.7206328374934152 2 1 3.7269849963023267 0 0 0
+9 3 0.6063699309305985 0.04682595158675571 1.2335049647817748 2 1 3.7269849963023267 0 0 0
+10 4 0.8003979559814726 -0.364393011459011 0.9884025318908612 2 1 3.7269849963023267 0 0 0
+
+Velocities
+
+1 0.320321385294804 -0.13632815939410442 -0.029398292452023418 0.3064009492028237 -0.15808560233691588 0.35878007201886397
+2 0.16868594667473025 -0.04950805613064363 0.15811007290373785 -0.07666583909321756 -0.0008074676325318194 -0.21475821019816385
+3 -0.22924557018300165 0.08381876748892438 -0.0919832851533896 0.4039387481683193 0.6123610642545824 -0.11063432848545783
+4 -0.22186204313310393 0.04952817499985707 -0.0693642101605732 -0.1358248430264938 0.4118493572385653 -0.056529305922687775
+5 0.08156431270087049 -0.2564594759800144 0.1724544416027875 0.05439894663158808 0.09338481510384318 0.3205408219238883
+6 0.03598698404367743 -0.04868642973674152 0.02860105256592922 0.04007709957283992 -0.317943400069374 0.36438025397586354
+7 -0.00822868972307372 0.047514932936351305 -0.027726409420297023 0.18356392696891796 -0.49877294396308003 0.06993313839189567
+8 -0.07177147672242379 0.1718272727853115 0.39056151182616994 -0.16728362538690794 -0.47839708820957955 -0.17897249005947627
+9 -0.1748638855727651 -0.0781638161351808 0.0560181565271157 -0.28062568580131014 0.2405396522734162 -0.4311598357169048
+10 0.18870318272756448 -0.1066780134639517 0.12610657946741227 -0.05740397100183697 0.36748833227892685 0.1498775724372025
+
+Bonds
+
+1 1 1 2
+2 1 2 3
+3 1 3 4
+4 1 4 5
+5 1 6 7
+6 1 7 8
+7 1 8 9
+8 1 9 10
+
+Ellipsoids
+
+1 1.173984503142341 1.173984503142341 1.173984503142341 0.9890278201757743 0.01779228232037064 -0.14337734159225404 0.030827642240801516
+2 1.173984503142341 1.173984503142341 1.173984503142341 0.939687458852748 0.04174166924055095 -0.023337773785056866 0.338674565089608
+3 1.173984503142341 1.173984503142341 1.173984503142341 0.8210113150655425 0.03012140921736572 0.017666019956944813 0.5698429897612057
+4 1.173984503142341 1.173984503142341 1.173984503142341 0.6623662858285051 -0.028186343967346823 0.022942552517501488 0.7482981175276918
+5 1.173984503142341 1.173984503142341 1.173984503142341 0.3601488726765216 0.0513614985821682 0.0724224158335286 0.9286602067807472
+6 1.173984503142341 1.173984503142341 1.173984503142341 0.11941234710084649 0.9244660117493703 -0.35317942248051865 -0.07979711784524246
+7 1.173984503142341 1.173984503142341 1.173984503142341 -0.17949125421205164 0.7412884899431119 -0.6379094464220707 0.1065166771202199
+8 1.173984503142341 1.173984503142341 1.173984503142341 -0.10483691088405202 0.5508895999584645 -0.8250090480220789 0.06992811634525403
+9 1.173984503142341 1.173984503142341 1.173984503142341 0.07777239911646 -0.3724087549185288 0.9103052384821374 -0.1631181963720798
+10 1.173984503142341 1.173984503142341 1.173984503142341 0.16279109707978262 0.027148630125149613 0.9849325709665359 -0.0516705065113425

examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/potential_file/data.duplex1

@@ -0,0 +1,68 @@
+LAMMPS data file via write_data, version 27 May 2021
+
+10 atoms
+4 atom types
+8 bonds
+1 bond types
+10 ellipsoids
+
+-20 20 xlo xhi
+-20 20 ylo yhi
+-20 20 zlo zhi
+
+Masses
+
+1 3.1575
+2 3.1575
+3 3.1575
+4 3.1575
+
+Atoms # hybrid
+
+1 1 -0.33741452300167507 -0.43708835412476305 0.6450685042019271 1 1 3.7269849963023267 0 0 0
+2 2 -0.32142606102826937 -0.7137743037592722 1.1817366147004618 1 1 3.7269849963023267 0 0 0
+3 3 -0.130363628207774 -0.9147144801536078 1.62581312195109 1 1 3.7269849963023267 0 0 0
+4 4 0.16795127962282844 -0.9808507459807022 2.0894908590909003 1 1 3.7269849963023267 0 0 0
+5 1 0.46370423490634166 -0.7803347954883079 2.4251986815515827 1 1 3.7269849963023267 0 0 0
+6 4 -0.4462950185476711 0.09062163051035639 2.4668941268777607 2 1 3.7269849963023267 0 0 0
+7 1 -0.03377054097560965 0.20979847489755046 2.078208732038921 2 1 3.7269849963023267 0 0 0
+8 2 0.3297325391466579 0.17657587120899895 1.7206328374934152 2 1 3.7269849963023267 0 0 0
+9 3 0.6063699309305985 0.04682595158675571 1.2335049647817748 2 1 3.7269849963023267 0 0 0
+10 4 0.8003979559814726 -0.364393011459011 0.9884025318908612 2 1 3.7269849963023267 0 0 0
+
+Velocities
+
+1 0.320321385294804 -0.13632815939410442 -0.029398292452023418 0.3064009492028237 -0.15808560233691588 0.35878007201886397
+2 0.16868594667473025 -0.04950805613064363 0.15811007290373785 -0.07666583909321756 -0.0008074676325318194 -0.21475821019816385
+3 -0.22924557018300165 0.08381876748892438 -0.0919832851533896 0.4039387481683193 0.6123610642545824 -0.11063432848545783
+4 -0.22186204313310393 0.04952817499985707 -0.0693642101605732 -0.1358248430264938 0.4118493572385653 -0.056529305922687775
+5 0.08156431270087049 -0.2564594759800144 0.1724544416027875 0.05439894663158808 0.09338481510384318 0.3205408219238883
+6 0.03598698404367743 -0.04868642973674152 0.02860105256592922 0.04007709957283992 -0.317943400069374 0.36438025397586354
+7 -0.00822868972307372 0.047514932936351305 -0.027726409420297023 0.18356392696891796 -0.49877294396308003 0.06993313839189567
+8 -0.07177147672242379 0.1718272727853115 0.39056151182616994 -0.16728362538690794 -0.47839708820957955 -0.17897249005947627
+9 -0.1748638855727651 -0.0781638161351808 0.0560181565271157 -0.28062568580131014 0.2405396522734162 -0.4311598357169048
+10 0.18870318272756448 -0.1066780134639517 0.12610657946741227 -0.05740397100183697 0.36748833227892685 0.1498775724372025
+
+Bonds
+
+1 1 1 2
+2 1 2 3
+3 1 3 4
+4 1 4 5
+5 1 6 7
+6 1 7 8
+7 1 8 9
+8 1 9 10
+
+Ellipsoids
+
+1 1.173984503142341 1.173984503142341 1.173984503142341 0.9890278201757743 0.01779228232037064 -0.14337734159225404 0.030827642240801516
+2 1.173984503142341 1.173984503142341 1.173984503142341 0.939687458852748 0.04174166924055095 -0.023337773785056866 0.338674565089608
+3 1.173984503142341 1.173984503142341 1.173984503142341 0.8210113150655425 0.03012140921736572 0.017666019956944813 0.5698429897612057
+4 1.173984503142341 1.173984503142341 1.173984503142341 0.6623662858285051 -0.028186343967346823 0.022942552517501488 0.7482981175276918
+5 1.173984503142341 1.173984503142341 1.173984503142341 0.3601488726765216 0.0513614985821682 0.0724224158335286 0.9286602067807472
+6 1.173984503142341 1.173984503142341 1.173984503142341 0.11941234710084649 0.9244660117493703 -0.35317942248051865 -0.07979711784524246
+7 1.173984503142341 1.173984503142341 1.173984503142341 -0.17949125421205164 0.7412884899431119 -0.6379094464220707 0.1065166771202199
+8 1.173984503142341 1.173984503142341 1.173984503142341 -0.10483691088405202 0.5508895999584645 -0.8250090480220789 0.06992811634525403
+9 1.173984503142341 1.173984503142341 1.173984503142341 0.07777239911646 -0.3724087549185288 0.9103052384821374 -0.1631181963720798
+10 1.173984503142341 1.173984503142341 1.173984503142341 0.16279109707978262 0.027148630125149613 0.9849325709665359 -0.0516705065113425

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

@@ -0,0 +1,72 @@
+variable number equal 1
+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.duplex1
+
+set atom * mass 3.1575
+
+group all type 1 4
+
+# oxDNA2 bond interactions - FENE backbone
+bond_style oxdna2/fene
+bond_coeff * oxdna2_lj.cgdna
+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    oxdna2_lj.cgdna
+pair_coeff * * oxdna2/stk     seqdep 0.1 1.3523 2.6717 oxdna2_lj.cgdna
+pair_coeff * * oxdna2/hbond   seqdep oxdna2_lj.cgdna
+pair_coeff 1 4 oxdna2/hbond   seqdep oxdna2_lj.cgdna
+pair_coeff 2 3 oxdna2/hbond   seqdep oxdna2_lj.cgdna
+pair_coeff * * oxdna2/xstk    oxdna2_lj.cgdna
+pair_coeff * * oxdna2/coaxstk oxdna2_lj.cgdna
+pair_coeff * * oxdna2/dh      0.1 0.5 oxdna2_lj.cgdna
+
+# 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 1000000
+
+write_data last_config.${number}.* nocoeff
+#write_restart last_config.${number}.*

examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/potential_file/oxdna2_lj.cgdna

@@ -0,0 +1 @@
+../../../../../../../potentials/oxdna2_lj.cgdna

examples/PACKAGES/cgdna/examples/lj_units/oxRNA2/potential_file/data.duplex2

@@ -0,0 +1,91 @@
+LAMMPS data file via write_data, version 27 May 2021
+
+16 atoms
+4 atom types
+13 bonds
+1 bond types
+16 ellipsoids
+
+-20 20 xlo xhi
+-20 20 ylo yhi
+-20 20 zlo zhi
+
+Masses
+
+1 3.1575
+2 3.1575
+3 3.1575
+4 3.1575
+
+Atoms # hybrid
+
+1 1 -0.6133472972454725 -0.657478171669766 0.36065226351201896 1 1 3.7269849963023267 0 0 0
+2 2 -0.45262764247356363 -1.0030650534345913 0.7258693379233347 1 1 3.7269849963023267 0 0 0
+3 3 -0.0988342108522641 -1.239775807128057 1.069462285786363 1 1 3.7269849963023267 0 0 0
+4 4 0.2937771854299732 -1.2579750924899842 1.4258916086606965 1 1 3.7269849963023267 0 0 0
+5 1 0.6286896795685137 -1.0183343395119744 1.7689346339672825 1 1 3.7269849963023267 0 0 0
+6 2 0.7901522619067926 -0.6766341805565266 2.1540160705495754 1 1 3.7269849963023267 0 0 0
+7 3 0.7115777184886863 -0.40195579325143455 2.569568683291525 1 1 3.7269849963023267 0 0 0
+8 4 0.46973310377005234 -0.30251697967107033 3.0668007117519216 1 1 3.7269849963023267 0 0 0
+9 1 0.4056113349449848 -1.443775499211898 3.0590726503341124 2 1 3.7269849963023267 0 0 0
+10 2 -0.032028429059287516 -1.2947520971164723 2.7201071151392187 2 1 3.7269849963023267 0 0 0
+11 3 -0.31613855112314065 -0.908414175906161 2.4125207871782006 2 1 3.7269849963023267 0 0 0
+12 4 -0.38939391251821 -0.4866605488242819 2.006177777000426 2 1 3.7269849963023267 0 0 0
+13 1 -0.06232643040853296 -0.07155965522127403 1.5593206052730733 3 1 3.7269849963023267 0 0 0
+14 2 0.17884090390913376 -0.05516721349427172 1.021273149730912 3 1 3.7269849963023267 0 0 0
+15 3 0.4513439961906 -0.23795607383274572 0.5957328539615993 3 1 3.7269849963023267 0 0 0
+16 4 0.5077649359807965 -0.5565625134533538 0.1655875784458841 3 1 3.7269849963023267 0 0 0
+
+Velocities
+
+1 0.05386890022865587 0.02262922525602673 0.24882291144736746 0.1772010258006941 -0.29588531700001014 -0.2624137503614725
+2 -0.03995003075629463 0.26969511063701984 -0.18986454548195664 -0.030614539375968176 -0.11769518931480599 0.040074702426473215
+3 -0.20784535295201376 -0.13628722357673043 -0.06062477950201746 -0.03676034584820381 -0.06308707793373186 -0.14798601576087625
+4 -0.23969824181316998 -0.5624721730878831 0.032474422905036715 -0.16523645965016515 0.2860623077030974 0.33543519753105877
+5 -0.16114897356828353 -0.22889697470760145 -0.13553324962649563 0.07151030852881342 -0.09415592891043179 0.13422881539312292
+6 -0.04701706588477693 0.19216715585110036 0.14588242791297215 0.09218622989776322 -0.5640128930702024 0.09287105657777776
+7 0.05098438305112513 -0.038459555522009595 -0.14244196285749675 0.3479046835475834 0.4244922695910593 -0.13582882604358357
+8 0.37827971348411926 -0.04953992506010833 0.1626392045834847 0.0442887659636129 0.07868414126013584 -0.12713600444325032
+9 0.04912038408665491 0.041260647318716696 0.012223856334495234 0.03282916621721876 -0.00012670547095256 0.155978785417696
+10 0.1939216183073483 0.11075235485381942 -0.0405050516019971 -0.17008135001813812 -0.4563093565840761 -0.30318513627039506
+11 -0.351360733920646 -0.18822419067535692 0.36147938199051305 -0.3708221604627426 -0.49108381825941216 0.09435948331955418
+12 -0.1188642917357977 0.22355282456551884 0.009265586122144348 -0.28230100188858365 0.10276485660828892 0.10175233476780697
+13 -0.1446616296238799 -0.11552059909787235 0.1331477187595642 -0.25498721890374343 0.2754663721641154 0.05806416868630132
+14 0.051547120035862544 -0.36611026510775635 -0.06630782880801242 -0.11999847173316518 0.0684476892288605 0.2161595932308759
+15 -0.20214244962091388 0.23341226933559608 0.008133374252278069 -0.17013911124135248 0.01870292260510287 -0.2682954134361106
+16 -0.19202131162868008 -0.08105295741355378 -0.0469350810885074 0.017332107652647588 -0.32876588862807693 0.1085334141225924
+
+Bonds
+
+1 1 1 2
+2 1 2 3
+3 1 3 4
+4 1 4 5
+5 1 5 6
+6 1 6 7
+7 1 7 8
+8 1 9 10
+9 1 10 11
+10 1 11 12
+11 1 13 14
+12 1 14 15
+13 1 15 16
+
+Ellipsoids
+
+1 1.173984503142341 1.173984503142341 1.173984503142341 0.9964752158482045 -0.053253555733239796 0.011391163807102514 -0.06380787090289707
+2 1.173984503142341 1.173984503142341 1.173984503142341 0.9369923833143513 0.11220716044648564 0.06732538499716349 0.3239168400846305
+3 1.173984503142341 1.173984503142341 1.173984503142341 0.797964932091827 0.14473096354527873 0.18374142699366386 0.5554673737937029
+4 1.173984503142341 1.173984503142341 1.173984503142341 0.5660864821344559 0.14688275499481052 0.09873742533340191 0.8051226439917721
+5 1.173984503142341 1.173984503142341 1.173984503142341 0.2533023785125306 0.12062313161679827 0.08583012223905846 0.9559922359911086
+6 1.173984503142341 1.173984503142341 1.173984503142341 -0.03855807343534716 0.08405913137017908 0.02236505169306371 0.9954632800204194
+7 1.173984503142341 1.173984503142341 1.173984503142341 -0.45592844330248017 0.1004550065061007 -0.052524745294758785 0.8827679181910482
+8 1.173984503142341 1.173984503142341 1.173984503142341 0.768021221540491 -0.009582139884533599 0.03658677589040892 -0.63930665074644
+9 1.173984503142341 1.173984503142341 1.173984503142341 -0.23299975754512345 0.688686395231341 0.6747873944883376 -0.12682324016841584
+10 1.173984503142341 1.173984503142341 1.173984503142341 -0.24662061871907232 0.8744456399178389 0.39370836087823996 -0.13970261209395163
+11 1.173984503142341 1.173984503142341 1.173984503142341 -0.087475900850909 0.977367602388229 0.14493549113095577 -0.12686307572668784
+12 1.173984503142341 1.173984503142341 1.173984503142341 -0.03181169300779214 0.9634374984140112 -0.2442360692534371 -0.10547485630879185
+13 1.173984503142341 1.173984503142341 1.173984503142341 -0.032786070696572266 0.7922941528811777 -0.6084214170523915 -0.03191282109962717
+14 1.173984503142341 1.173984503142341 1.173984503142341 0.047188686288341455 0.6316396208287698 -0.7737349519945348 0.011783095844627799
+15 1.173984503142341 1.173984503142341 1.173984503142341 -0.05869980642620335 -0.34229358203414423 0.9376740835056508 0.012519965878508689
+16 1.173984503142341 1.173984503142341 1.173984503142341 -0.08582818143150042 0.0008707732197394232 0.9939540921464659 -0.0684691735853161

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

@@ -0,0 +1,73 @@
+variable number equal 2
+variable ofreq  equal 1000
+variable efreq  equal 1000
+variable T      equal 0.1
+variable rhos   equal 0.5
+
+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.duplex2
+
+set atom * mass 3.1575
+
+group all type 1 4
+
+# oxRNA2 bond interactions - FENE backbone
+bond_style oxrna2/fene
+bond_coeff * oxrna2_lj.cgdna
+special_bonds lj 0 1 1
+
+# oxRNA2 pair interactions
+pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh
+pair_coeff * * oxrna2/excv    oxrna2_lj.cgdna
+pair_coeff * * oxrna2/stk     seqdep 0.1 1.40206 2.77 oxrna2_lj.cgdna
+pair_coeff * * oxrna2/hbond   seqdep oxrna2_lj.cgdna
+pair_coeff 1 4 oxrna2/hbond   seqdep oxrna2_lj.cgdna
+pair_coeff 2 3 oxrna2/hbond   seqdep oxrna2_lj.cgdna
+pair_coeff 3 4 oxrna2/hbond   seqdep oxrna2_lj.cgdna
+pair_coeff * * oxrna2/xstk    oxrna2_lj.cgdna
+pair_coeff * * oxrna2/coaxstk oxrna2_lj.cgdna
+pair_coeff * * oxrna2/dh      0.1 0.5 oxrna2_lj.cgdna
+
+# 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 1000000
+
+write_data last_config.${number}.* nocoeff
+#write_restart last_config.${number}.*

examples/PACKAGES/cgdna/examples/lj_units/oxRNA2/potential_file/oxrna2_lj.cgdna

@@ -0,0 +1 @@
+../../../../../../../potentials/oxrna2_lj.cgdna

examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex1/data.duplex1

@@ -0,0 +1,68 @@
+LAMMPS data file in real units via oxdna lj2real.py, date 2024-05-19
+
+10 atoms
+4 atom types
+8 bonds
+1 bond types
+10 ellipsoids
+
+-170 170 xlo xhi
+-170 170 ylo yhi
+-170 170 zlo zhi
+
+Masses
+
+1 315.8376
+2 315.8376
+3 315.8376
+4 315.8376
+
+Atoms # hybrid
+
+1 1 -2.8740969069282687 -3.723118600434732 5.494693518792015 1 1 1.0016462505133576 0 0 0
+2 2 -2.7379071878387986 -6.079929519421481 10.066032484018534 1 1 1.0016462505133576 0 0 0
+3 3 -1.110437385073819 -7.791537941948432 13.848676172779387 1 1 1.0016462505133576 0 0 0
+4 4 1.4306089998272526 -8.354886654263622 17.79828313773629 1 1 1.0016462505133576 0 0 0
+5 1 3.9498326729322186 -6.646891787969407 20.657842369456382 1 1 1.0016462505133576 0 0 0
+6 4 -3.801540967989063 0.7719150486872158 21.01300417274477 2 1 1.0016462505133576 0 0 0
+7 1 -0.287657468030243 1.787063409177335 17.702181979507532 2 1 1.0016462505133576 0 0 0
+8 2 2.8086617684512323 1.5040732709582532 14.656350509768911 2 1 1.0016462505133576 0 0 0
+9 3 5.165059071666839 0.3988634556159852 10.50699529001116 2 1 1.0016462505133576 0 0 0
+10 4 6.817789789050184 -3.1038996716078557 8.419212766646357 2 1 1.0016462505133576 0 0 0
+
+Velocities
+
+1 0.0015993537866009029 -0.000680681865016988 -0.00014678467473993874 1.3034875452014287 -0.6725260292370423 1.5263182328899618
+2 0.0008422431968202534 -0.0002471920411024751 0.0007894382186365997 -0.32615096872390803 -0.0034351199136194157 -0.9136220137417161
+3 -0.0011446153381118452 0.00041850425643063176 -0.00045926941555484915 1.7184317758530245 2.6050996986101502 -0.47065934236730145
+4 -0.0011077496385743138 0.0002472924939324634 -0.00034633314311123244 -0.5778245520276679 1.752085001878762 -0.24048635097513535
+5 0.0004072478403200556 -0.0012804934445473403 0.0008610591638760516 0.23142339993018143 0.3972766524238825 1.363641236078021
+6 0.00017968178785700138 -0.00024308968845109275 0.00014280408309295725 0.1704955558294103 -1.3525913126172677 1.5501424653239764
+7 -4.108556803115003e-05 0.00023724044475488887 -0.00013843701960263193 0.7809156374181498 -2.1218743676572576 0.2975087875146955
+8 -0.00035835254321313353 0.0008579277312926632 0.0019500603503724006 -0.711656157643413 -2.0351916264105014 -0.7613827970610736
+9 -0.0008730894357027041 -0.00039026927657647716 0.0002796967510539106 -1.193834703375802 1.023301140813147 -1.8342354268493246
+10 0.0009421885758929626 -0.0005326396944231774 0.0006296458639527654 -0.24420734152643714 1.5633648178267814 0.6376075187926279
+
+Bonds
+
+1 1 1 2
+2 1 2 3
+3 1 3 4
+4 1 4 5
+5 1 6 7
+6 1 7 8
+7 1 8 9
+8 1 9 10
+
+Ellipsoids
+
+1 9.999999997766462 9.999999997766462 9.999999997766462 0.9890278201757743 0.01779228232037064 -0.14337734159225404 0.030827642240801516
+2 9.999999997766462 9.999999997766462 9.999999997766462 0.939687458852748 0.04174166924055095 -0.023337773785056866 0.338674565089608
+3 9.999999997766462 9.999999997766462 9.999999997766462 0.8210113150655425 0.03012140921736572 0.017666019956944813 0.5698429897612057
+4 9.999999997766462 9.999999997766462 9.999999997766462 0.6623662858285051 -0.028186343967346823 0.022942552517501488 0.7482981175276918
+5 9.999999997766462 9.999999997766462 9.999999997766462 0.3601488726765216 0.0513614985821682 0.0724224158335286 0.9286602067807472
+6 9.999999997766462 9.999999997766462 9.999999997766462 0.11941234710084649 0.9244660117493703 -0.35317942248051865 -0.07979711784524246
+7 9.999999997766462 9.999999997766462 9.999999997766462 -0.17949125421205164 0.7412884899431119 -0.6379094464220707 0.1065166771202199
+8 9.999999997766462 9.999999997766462 9.999999997766462 -0.10483691088405202 0.5508895999584645 -0.8250090480220789 0.06992811634525403
+9 9.999999997766462 9.999999997766462 9.999999997766462 0.07777239911646 -0.3724087549185288 0.9103052384821374 -0.1631181963720798
+10 9.999999997766462 9.999999997766462 9.999999997766462 0.16279109707978262 0.027148630125149613 0.9849325709665359 -0.0516705065113425

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

@@ -0,0 +1,71 @@
+# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19
+variable number	equal 1
+variable ofreq	equal 1000
+variable efreq	equal 1000
+variable T      equal 300.0
+
+units real
+
+dimension 3
+
+newton on
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid oxdna
+atom_modify sort 0 8.518
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 17.036 bin
+neigh_modify every 1 delay 0 check yes
+
+read_data data.duplex1
+
+set atom * mass 315.8376
+
+group all type 1 4
+
+# oxDNA bond interactions - FENE backbone
+bond_style oxdna/fene
+bond_coeff * 11.92337812042065 2.1295 6.409795
+special_bonds lj 0 1 1
+
+# oxDNA pair interactions
+pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
+pair_coeff * * oxdna/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576
+pair_coeff * * oxdna/stk seqav ${T} 8.01727944817084 0.005279604 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna/hbond seqav 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
+pair_coeff 1 4 oxdna/hbond seqav 6.42073911784652 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
+pair_coeff 2 3 oxdna/hbond seqav 6.42073911784652 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
+pair_coeff * * oxdna/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 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 * * oxdna/coaxstk 3.77965257404268 3.4072 5.1108 1.87396 4.94044 2.0 2.541592654 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2 -0.65 2 -0.65
+
+# NVE ensemble
+fix 1 all nve/asphere
+#fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10
+
+timestep 0.01706
+
+#comm_style tiled
+fix 3 all balance 1000 1.03 shift xyz 10 1.03
+comm_modify cutoff 32.4
+
+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 1000000
+
+write_data last_config.${number}.* nocoeff
+#write_restart last_config.${number}.*

examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex2/data.duplex2

@@ -0,0 +1,91 @@
+LAMMPS data file in real units via oxdna lj2real.py, date 2024-05-19
+
+16 atoms
+4 atom types
+13 bonds
+1 bond types
+16 ellipsoids
+
+-170 170 xlo xhi
+-170 170 ylo yhi
+-170 170 zlo zhi
+
+Masses
+
+1 315.8376
+2 315.8376
+3 315.8376
+4 315.8376
+
+Atoms # hybrid
+
+1 1 -5.224492277936935 -5.6003990662830665 3.072035980595378 1 1 1.0016462505133576 0 0 0
+2 2 -3.855482258589815 -8.54410812515585 6.182955020430966 1 1 1.0016462505133576 0 0 0
+3 3 -0.8418698080395857 -10.56041032511679 9.10967975032824 1 1 1.0016462505133576 0 0 0
+4 4 2.502394065492512 -10.715431837829685 12.145744722571814 1 1 1.0016462505133576 0 0 0
+5 1 5.355178690564601 -8.674171903962998 15.067785212133312 1 1 1.0016462505133576 0 0 0
+6 2 6.7305169669220595 -5.763569949980494 18.347908888941284 1 1 1.0016462505133576 0 0 0
+7 3 6.061219006086631 -3.4238594469157198 21.88758604427721 1 1 1.0016462505133576 0 0 0
+8 4 4.001186577913306 -2.576839632838177 26.12300846270287 1 1 1.0016462505133576 0 0 0
+9 1 3.454997351061381 -12.298079702286948 26.05718083554597 2 1 1.0016462505133576 0 0 0
+10 2 -0.2728181587270111 -11.028698363238112 23.169872406755868 2 1 1.0016462505133576 0 0 0
+11 3 -2.692868178466912 -7.73787195036868 20.549852065183913 2 1 1.0016462505133576 0 0 0
+12 4 -3.316857346830113 -4.145374554885233 17.08862230448963 2 1 1.0016462505133576 0 0 0
+13 1 -0.5308965342198838 -0.6095451431748122 13.28229291571604 3 1 1.0016462505133576 0 0 0
+14 2 1.5233668194980015 -0.46991432454420656 8.699204689407908 3 1 1.0016462505133576 0 0 0
+15 3 3.844548159551531 -2.026909836907328 5.074452450044903 3 1 1.0016462505133576 0 0 0
+16 4 4.325141724684425 -4.740799489595668 1.4104749932020408 3 1 1.0016462505133576 0 0 0
+
+Velocities
+
+1 0.00026896558742537556 0.00011298695236274073 0.001242364337461123 0.7538466533118467 -1.2587520584415195 -1.1163576881067447
+2 -0.00019946914535880285 0.0013465785184092233 -0.0009479872206420321 -0.13024003640483983 -0.5006975787807386 0.17048535791572514
+3 -0.0010377647810347322 -0.0006804774738725614 -0.000302697462953215 -0.15638545864527348 -0.2683843524758034 -0.6295604792026762
+4 -0.0011968051721949484 -0.002808404437492725 0.00016214368951061121 -0.7029471277015998 1.2169631204234201 1.42700472482703
+5 -0.0008046113463391788 -0.001142874812754601 -0.0006767129075723855 0.304218367349499 -0.4005571162913614 0.5710347488390389
+6 -0.00023475461149269044 0.000959484075931813 0.0007283860029089665 0.3921776444343422 -2.399417440979843 0.3950910265578085
+7 0.0002545632912247854 -0.00019202725318668095 -0.0007112078778547229 1.4800522749729792 1.8058703404340948 -0.5778414965351256
+8 0.0018887377488028885 -0.0002473511615838234 0.0008120520191337178 0.18841278062652408 0.3347372075847072 -0.5408605905745774
+9 0.0002452564077667799 0.00020601300929708606 6.1033299095680186e-05 0.13966147753401867 -0.0005390290197378453 0.6635632318913824
+10 0.000968244047328249 0.0005529827424647325 -0.00020224034557198784 -0.7235582069719148 -1.9412262416735993 -1.289806869224333
+11 -0.0017543321990246556 -0.000939796984860897 0.0018048542648271923 -1.5775475529872025 -2.0891633737315023 0.40142307521789933
+12 -0.0005934853675296159 0.001116191652783757 4.626275649966328e-05 -1.200961814632207 0.4371811217355096 0.43287366246768927
+13 -0.0007222905985558083 -0.0005767904238661645 0.0006648020330562531 -1.084763819731394 1.1718860080947717 0.2470159472481526
+14 0.0002573730178578412 -0.00182797610679242 -0.00033107273492769625 -0.510496177490122 0.29118940603730814 0.9195837620128926
+15 -0.0010092903785878923 0.0011654195253227475 4.0609661125969864e-05 -0.723803934131871 0.07956576746268508 -1.1413793944128399
+16 -0.0009587558806876301 -0.0004046946607553641 -0.0002343452641922075 0.07373406158203998 -1.3986322243084912 0.4617216556119086
+
+Bonds
+
+1 1 1 2
+2 1 2 3
+3 1 3 4
+4 1 4 5
+5 1 5 6
+6 1 6 7
+7 1 7 8
+8 1 9 10
+9 1 10 11
+10 1 11 12
+11 1 13 14
+12 1 14 15
+13 1 15 16
+
+Ellipsoids
+
+1 9.999999997766462 9.999999997766462 9.999999997766462 0.9964752158482045 -0.053253555733239796 0.011391163807102514 -0.06380787090289707
+2 9.999999997766462 9.999999997766462 9.999999997766462 0.9369923833143513 0.11220716044648564 0.06732538499716349 0.3239168400846305
+3 9.999999997766462 9.999999997766462 9.999999997766462 0.797964932091827 0.14473096354527873 0.18374142699366386 0.5554673737937029
+4 9.999999997766462 9.999999997766462 9.999999997766462 0.5660864821344559 0.14688275499481052 0.09873742533340191 0.8051226439917721
+5 9.999999997766462 9.999999997766462 9.999999997766462 0.2533023785125306 0.12062313161679827 0.08583012223905846 0.9559922359911086
+6 9.999999997766462 9.999999997766462 9.999999997766462 -0.03855807343534716 0.08405913137017908 0.02236505169306371 0.9954632800204194
+7 9.999999997766462 9.999999997766462 9.999999997766462 -0.45592844330248017 0.1004550065061007 -0.052524745294758785 0.8827679181910482
+8 9.999999997766462 9.999999997766462 9.999999997766462 0.768021221540491 -0.009582139884533599 0.03658677589040892 -0.63930665074644
+9 9.999999997766462 9.999999997766462 9.999999997766462 -0.23299975754512345 0.688686395231341 0.6747873944883376 -0.12682324016841584
+10 9.999999997766462 9.999999997766462 9.999999997766462 -0.24662061871907232 0.8744456399178389 0.39370836087823996 -0.13970261209395163
+11 9.999999997766462 9.999999997766462 9.999999997766462 -0.087475900850909 0.977367602388229 0.14493549113095577 -0.12686307572668784
+12 9.999999997766462 9.999999997766462 9.999999997766462 -0.03181169300779214 0.9634374984140112 -0.2442360692534371 -0.10547485630879185
+13 9.999999997766462 9.999999997766462 9.999999997766462 -0.032786070696572266 0.7922941528811777 -0.6084214170523915 -0.03191282109962717
+14 9.999999997766462 9.999999997766462 9.999999997766462 0.047188686288341455 0.6316396208287698 -0.7737349519945348 0.011783095844627799
+15 9.999999997766462 9.999999997766462 9.999999997766462 -0.05869980642620335 -0.34229358203414423 0.9376740835056508 0.012519965878508689
+16 9.999999997766462 9.999999997766462 9.999999997766462 -0.08582818143150042 0.0008707732197394232 0.9939540921464659 -0.0684691735853161

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

@@ -0,0 +1,71 @@
+# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19
+variable number	equal 2
+variable ofreq	equal 1000
+variable efreq	equal 1000
+variable T      equal 300.0
+
+units real
+
+dimension 3
+
+newton on
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid oxdna
+atom_modify sort 0 8.518
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 17.036 bin
+neigh_modify every 1 delay 0 check yes
+
+read_data data.duplex2
+
+set atom * mass 315.8376
+
+group all type 1 4
+
+# oxDNA bond interactions - FENE backbone
+bond_style oxdna/fene
+bond_coeff * 11.92337812042065 2.1295 6.409795
+special_bonds lj 0 1 1
+
+# oxDNA pair interactions
+pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
+pair_coeff * * oxdna/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576
+pair_coeff * * oxdna/stk seqav ${T} 8.01727944817084 0.005279604 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna/hbond seqav 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
+pair_coeff 1 4 oxdna/hbond seqav 6.42073911784652 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
+pair_coeff 2 3 oxdna/hbond seqav 6.42073911784652 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
+pair_coeff * * oxdna/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 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 * * oxdna/coaxstk 3.77965257404268 3.4072 5.1108 1.87396 4.94044 2.0 2.541592654 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2 -0.65 2 -0.65
+
+# NVE ensemble
+fix 1 all nve/asphere
+fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10
+
+timestep 0.01706
+
+#comm_style tiled
+fix 3 all balance 1000 1.03 shift xyz 10 1.03
+comm_modify cutoff 32.4
+
+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 1000000
+
+write_data last_config.${number}.* nocoeff
+#write_restart last_config.${number}.*

examples/PACKAGES/cgdna/examples/real_units/oxDNA/potential_file/data.duplex1

@@ -0,0 +1,68 @@
+LAMMPS data file in real units via oxdna lj2real.py, date 2024-05-19
+
+10 atoms
+4 atom types
+8 bonds
+1 bond types
+10 ellipsoids
+
+-170 170 xlo xhi
+-170 170 ylo yhi
+-170 170 zlo zhi
+
+Masses
+
+1 315.8376
+2 315.8376
+3 315.8376
+4 315.8376
+
+Atoms # hybrid
+
+1 1 -2.8740969069282687 -3.723118600434732 5.494693518792015 1 1 1.0016462505133576 0 0 0
+2 2 -2.7379071878387986 -6.079929519421481 10.066032484018534 1 1 1.0016462505133576 0 0 0
+3 3 -1.110437385073819 -7.791537941948432 13.848676172779387 1 1 1.0016462505133576 0 0 0
+4 4 1.4306089998272526 -8.354886654263622 17.79828313773629 1 1 1.0016462505133576 0 0 0
+5 1 3.9498326729322186 -6.646891787969407 20.657842369456382 1 1 1.0016462505133576 0 0 0
+6 4 -3.801540967989063 0.7719150486872158 21.01300417274477 2 1 1.0016462505133576 0 0 0
+7 1 -0.287657468030243 1.787063409177335 17.702181979507532 2 1 1.0016462505133576 0 0 0
+8 2 2.8086617684512323 1.5040732709582532 14.656350509768911 2 1 1.0016462505133576 0 0 0
+9 3 5.165059071666839 0.3988634556159852 10.50699529001116 2 1 1.0016462505133576 0 0 0
+10 4 6.817789789050184 -3.1038996716078557 8.419212766646357 2 1 1.0016462505133576 0 0 0
+
+Velocities
+
+1 0.0015993537866009029 -0.000680681865016988 -0.00014678467473993874 1.3034875452014287 -0.6725260292370423 1.5263182328899618
+2 0.0008422431968202534 -0.0002471920411024751 0.0007894382186365997 -0.32615096872390803 -0.0034351199136194157 -0.9136220137417161
+3 -0.0011446153381118452 0.00041850425643063176 -0.00045926941555484915 1.7184317758530245 2.6050996986101502 -0.47065934236730145
+4 -0.0011077496385743138 0.0002472924939324634 -0.00034633314311123244 -0.5778245520276679 1.752085001878762 -0.24048635097513535
+5 0.0004072478403200556 -0.0012804934445473403 0.0008610591638760516 0.23142339993018143 0.3972766524238825 1.363641236078021
+6 0.00017968178785700138 -0.00024308968845109275 0.00014280408309295725 0.1704955558294103 -1.3525913126172677 1.5501424653239764
+7 -4.108556803115003e-05 0.00023724044475488887 -0.00013843701960263193 0.7809156374181498 -2.1218743676572576 0.2975087875146955
+8 -0.00035835254321313353 0.0008579277312926632 0.0019500603503724006 -0.711656157643413 -2.0351916264105014 -0.7613827970610736
+9 -0.0008730894357027041 -0.00039026927657647716 0.0002796967510539106 -1.193834703375802 1.023301140813147 -1.8342354268493246
+10 0.0009421885758929626 -0.0005326396944231774 0.0006296458639527654 -0.24420734152643714 1.5633648178267814 0.6376075187926279
+
+Bonds
+
+1 1 1 2
+2 1 2 3
+3 1 3 4
+4 1 4 5
+5 1 6 7
+6 1 7 8
+7 1 8 9
+8 1 9 10
+
+Ellipsoids
+
+1 9.999999997766462 9.999999997766462 9.999999997766462 0.9890278201757743 0.01779228232037064 -0.14337734159225404 0.030827642240801516
+2 9.999999997766462 9.999999997766462 9.999999997766462 0.939687458852748 0.04174166924055095 -0.023337773785056866 0.338674565089608
+3 9.999999997766462 9.999999997766462 9.999999997766462 0.8210113150655425 0.03012140921736572 0.017666019956944813 0.5698429897612057
+4 9.999999997766462 9.999999997766462 9.999999997766462 0.6623662858285051 -0.028186343967346823 0.022942552517501488 0.7482981175276918
+5 9.999999997766462 9.999999997766462 9.999999997766462 0.3601488726765216 0.0513614985821682 0.0724224158335286 0.9286602067807472
+6 9.999999997766462 9.999999997766462 9.999999997766462 0.11941234710084649 0.9244660117493703 -0.35317942248051865 -0.07979711784524246
+7 9.999999997766462 9.999999997766462 9.999999997766462 -0.17949125421205164 0.7412884899431119 -0.6379094464220707 0.1065166771202199
+8 9.999999997766462 9.999999997766462 9.999999997766462 -0.10483691088405202 0.5508895999584645 -0.8250090480220789 0.06992811634525403
+9 9.999999997766462 9.999999997766462 9.999999997766462 0.07777239911646 -0.3724087549185288 0.9103052384821374 -0.1631181963720798
+10 9.999999997766462 9.999999997766462 9.999999997766462 0.16279109707978262 0.027148630125149613 0.9849325709665359 -0.0516705065113425

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

@@ -0,0 +1,71 @@
+# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19
+variable number equal 1
+variable ofreq  equal 1000
+variable efreq  equal 1000
+variable T      equal 300.0
+
+units real
+
+dimension 3
+
+newton on
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid oxdna
+atom_modify sort 0 8.518
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 17.036 bin
+neigh_modify every 1 delay 0 check yes
+
+read_data data.duplex1
+
+set atom * mass 315.8376
+
+group all type 1 4
+
+# oxDNA bond interactions - FENE backbone
+bond_style oxdna/fene
+bond_coeff * oxdna_real.cgdna
+special_bonds lj 0 1 1
+
+# oxDNA pair interactions
+pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
+pair_coeff * * oxdna/excv    oxdna_real.cgdna
+pair_coeff * * oxdna/stk     seqav ${T} 8.01727944817084 0.005279604 oxdna_real.cgdna
+pair_coeff * * oxdna/hbond   seqav oxdna_real.cgdna
+pair_coeff 1 4 oxdna/hbond   seqav oxdna_real.cgdna
+pair_coeff 2 3 oxdna/hbond   seqav oxdna_real.cgdna
+pair_coeff * * oxdna/xstk    oxdna_real.cgdna
+pair_coeff * * oxdna/coaxstk oxdna_real.cgdna
+
+# NVE ensemble
+fix 1 all nve/asphere
+#fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10
+
+timestep 0.01706
+
+#comm_style tiled
+fix 3 all balance 1000 1.03 shift xyz 10 1.03
+comm_modify cutoff 32.4
+
+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 1000000
+
+write_data last_config.${number}.* nocoeff
+#write_restart last_config.${number}.*

examples/PACKAGES/cgdna/examples/real_units/oxDNA/potential_file/oxdna_real.cgdna

@@ -0,0 +1 @@
+../../../../../../../potentials/oxdna_real.cgdna

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

@@ -0,0 +1,622 @@
+LAMMPS data file in real units via oxdna lj2real.py, date 2024-05-19
+
+148 atoms
+4 atom types
+148 bonds
+1 bond types
+148 ellipsoids
+
+0 851 xlo xhi
+0 851 ylo yhi
+0 851 zlo zhi
+
+Masses
+
+1 315.8376
+2 315.8376
+3 315.8376
+4 315.8376
+
+Atoms # hybrid
+
+1 1 208.31885120063512 209.07830059400624 213.0216021921939 1 1 1.0016462505133576 0 0 0
+2 4 208.94483576838627 206.4448010919165 216.6882923344523 1 1 1.0016462505133576 0 0 0
+3 3 211.56385346871699 204.30406864289688 220.11920728875927 1 1 1.0016462505133576 0 0 0
+4 2 214.31495335572012 204.35063728809808 223.61677544780568 1 1 1.0016462505133576 0 0 0
+5 1 217.30951997235965 206.16090626093134 225.4674912137906 1 1 1.0016462505133576 0 0 0
+6 2 219.30502197188136 209.00909667501074 227.49674701236893 1 1 1.0016462505133576 0 0 0
+7 3 219.83292281044646 212.19753274141107 230.53026977239148 1 1 1.0016462505133576 0 0 0
+8 2 218.93091557749156 214.31473141418766 234.6931272540053 1 1 1.0016462505133576 0 0 0
+9 4 220.32518751145957 214.85183803522298 239.6469648355356 1 1 1.0016462505133576 0 0 0
+10 2 219.79275827382872 213.3404053532149 243.70006386710043 1 1 1.0016462505133576 0 0 0
+11 3 220.70928151349608 210.21381004200654 247.14815553587854 1 1 1.0016462505133576 0 0 0
+12 2 223.67193733154724 208.04535577836813 249.67978988879284 1 1 1.0016462505133576 0 0 0
+13 2 227.31016552169513 206.16686658451448 251.61597827076264 1 1 1.0016462505133576 0 0 0
+14 1 231.80592101718645 204.9336536048614 251.53105173903185 1 1 1.0016462505133576 0 0 0
+15 2 236.2250804923752 205.47987477011685 250.98539881261863 1 1 1.0016462505133576 0 0 0
+16 3 240.0068773257833 207.77004331975903 249.53594241966383 1 1 1.0016462505133576 0 0 0
+17 1 242.98566065658693 210.5462682234126 249.63496548893542 1 1 1.0016462505133576 0 0 0
+18 4 245.42888445426894 214.27953740691964 250.53493716205472 1 1 1.0016462505133576 0 0 0
+19 2 248.78751685377597 216.90541434653767 253.53160552044426 1 1 1.0016462505133576 0 0 0
+20 4 251.39963359406735 218.16175894319667 257.62870661099066 1 1 1.0016462505133576 0 0 0
+21 2 255.5677235249031 217.61926364274564 260.07819570237643 1 1 1.0016462505133576 0 0 0
+22 3 259.63024332567574 215.18262726567113 260.69715353283686 1 1 1.0016462505133576 0 0 0
+23 1 263.1457867599882 212.6433935962059 258.9487935453862 1 1 1.0016462505133576 0 0 0
+24 1 266.3827446371434 210.87213953618837 256.26055100860737 1 1 1.0016462505133576 0 0 0
+25 2 267.97463902393866 210.20760693366043 251.4251108047254 1 1 1.0016462505133576 0 0 0
+26 3 270.07811694250654 210.90888555541903 247.7392596432837 1 1 1.0016462505133576 0 0 0
+27 1 271.09287437447114 213.11656552311496 244.5712139335691 1 1 1.0016462505133576 0 0 0
+28 4 272.8644901379567 216.09853596389848 242.34668607897146 1 1 1.0016462505133576 0 0 0
+29 3 277.14925724680575 218.15361661850437 241.02448320337692 1 1 1.0016462505133576 0 0 0
+30 2 281.6281862385014 219.54423347807102 240.83577460409623 1 1 1.0016462505133576 0 0 0
+31 4 285.53553117381364 218.07611082158127 239.4456849189117 1 1 1.0016462505133576 0 0 0
+32 2 288.8938226529956 215.3666526766779 237.57548982559325 1 1 1.0016462505133576 0 0 0
+33 1 291.12514756370877 212.98912935663924 233.8324040870632 1 1 1.0016462505133576 0 0 0
+34 4 291.3890795510732 210.45844522291486 230.3986316964525 1 1 1.0016462505133576 0 0 0
+35 2 290.3105820760069 208.74036664050792 226.7042745336879 1 1 1.0016462505133576 0 0 0
+36 4 289.18201447621146 208.91363527052587 222.89820557251684 1 1 1.0016462505133576 0 0 0
+37 2 288.971153902218 209.4805264669763 218.28666756836168 1 1 1.0016462505133576 0 0 0
+38 4 288.3534988328343 212.6173536934077 215.1661607036478 1 1 1.0016462505133576 0 0 0
+39 3 290.5684723991064 215.9608847032356 212.4583306861778 1 1 1.0016462505133576 0 0 0
+40 1 292.68130870382674 219.40449003374115 209.55910765683777 1 1 1.0016462505133576 0 0 0
+41 4 295.442338041982 219.36246849520484 206.48916887364152 1 1 1.0016462505133576 0 0 0
+42 2 296.36417522086 218.26244483114334 201.69379456148616 1 1 1.0016462505133576 0 0 0
+43 1 296.0323698080443 215.8225532800091 197.3280985778793 1 1 1.0016462505133576 0 0 0
+44 4 294.6530843322007 212.83142447716733 193.82965995050543 1 1 1.0016462505133576 0 0 0
+45 4 293.09410894134015 209.80599344824577 192.16605946359905 1 1 1.0016462505133576 0 0 0
+46 2 288.83490978178446 208.30134671602775 191.4877951864582 1 1 1.0016462505133576 0 0 0
+47 3 284.41597526830526 208.24835045301987 190.80522332231112 1 1 1.0016462505133576 0 0 0
+48 3 280.435589003895 210.25289346065463 190.2013738364397 1 1 1.0016462505133576 0 0 0
+49 1 276.458218418495 212.91127251248324 189.31964814095224 1 1 1.0016462505133576 0 0 0
+50 4 274.110573437327 215.08405186209467 186.3098121169227 1 1 1.0016462505133576 0 0 0
+51 2 272.2617942946457 216.3726311673256 182.27450679276578 1 1 1.0016462505133576 0 0 0
+52 2 269.83153994135154 216.05780869626503 177.8206876525648 1 1 1.0016462505133576 0 0 0
+53 3 267.4176400816519 213.93217536542784 174.3937134479138 1 1 1.0016462505133576 0 0 0
+54 2 263.3829580061682 212.17957495128988 172.47054426846077 1 1 1.0016462505133576 0 0 0
+55 2 259.23622219283226 208.62789572578382 172.79202606983338 1 1 1.0016462505133576 0 0 0
+56 1 254.9232399751811 207.98723446147798 174.1700423374239 1 1 1.0016462505133576 0 0 0
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examples/PACKAGES/cgdna/examples/real_units/oxDNA2/dsring/in.dsring

@@ -0,0 +1,73 @@
+# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19
+variable number	equal 5
+variable ofreq	equal 1000
+variable efreq	equal 1000
+variable T      equal 300.0
+variable rhos   equal 0.2
+
+units real
+
+dimension 3
+
+newton on
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid oxdna
+atom_modify sort 0 8.518
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 17.036 bin
+neigh_modify every 1 delay 0 check yes
+
+read_data data.dsring
+
+set atom * mass 315.8376
+
+group all type 1 4
+
+# oxDNA2 bond interactions - FENE backbone
+bond_style oxdna2/fene
+bond_coeff * 11.92337812042065 2.1295 6.4430152
+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 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576
+pair_coeff * * oxdna2/stk seqdep ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
+pair_coeff 1 4 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
+pair_coeff 2 3 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
+pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 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 4.80673207785863 3.4072 5.1108 1.87396 4.94044 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} 4265.0 457145 angmom 10
+
+timestep 0.01706
+
+#comm_style tiled
+fix 3 all balance 1000 1.03 shift xyz 10 1.03
+comm_modify cutoff 32.4
+
+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/real_units/oxDNA2/dsring/log.22May24.dsring.g++.1

@@ -0,0 +1,286 @@
+LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified)
+# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19
+variable number	equal 5
+variable ofreq	equal 1000
+variable efreq	equal 1000
+variable T      equal 300.0
+variable rhos   equal 0.2
+
+units real
+
+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:132)
+atom_modify sort 0 8.518
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 17.036 bin
+neigh_modify every 1 delay 0 check yes
+
+read_data data.dsring
+Reading data file ...
+  orthogonal box = (0 0 0) to (851 851 851)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  148 atoms
+  reading velocities ...
+  148 velocities
+  scanning bonds ...
+  1 = max bonds/atom
+  148 ellipsoids
+  orthogonal box = (0 0 0) to (851 851 851)
+  1 by 1 by 1 MPI processor grid
+  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 = 0.012 seconds
+
+set atom * mass 315.8376
+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 * 11.92337812042065 2.1295 6.4430152
+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 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576
+pair_coeff * * oxdna2/stk seqdep ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/stk seqdep 300 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
+pair_coeff 1 4 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
+pair_coeff 2 3 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
+pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 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 4.80673207785863 3.4072 5.1108 1.87396 4.94044 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 300 ${rhos} 0.815
+pair_coeff * * oxdna2/dh 300 0.2 0.815
+
+# NVE ensemble
+fix 1 all nve/asphere
+#fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10
+
+timestep 0.01706
+
+#comm_style tiled
+fix 3 all balance 1000 1.03 shift xyz 10 1.03
+comm_modify cutoff 32.4
+
+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
+Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 48.032697
+  ghost atom cutoff = 48.032697
+  binsize = 24.016348, 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 48.03269686950012 (../comm.cpp:739)
+0  ekin = 122.015812851425 |  erot = 125.402528675609 | epot = -1325.18559882055 | etot = -1077.76725729351
+Per MPI rank memory allocation (min/avg/max) = 7.806 | 7.806 | 7.806 Mbytes
+   Step          Temp          E_pair         E_mol          TotEng         Press          Volume    
+         0   278.46107     -1367.7166      42.531022     -1203.1698     -0.0059756093   6.1629505e+08
+1000  ekin = 122.370905858635 |  erot = 126.447129514011 | epot = -1326.58529267981 | etot = -1077.76725730717
+2000  ekin = 122.691275133791 |  erot = 127.497291822809 | epot = -1327.95582427469 | etot = -1077.76725731809
+3000  ekin = 122.920677842253 |  erot = 128.459039892254 | epot = -1329.14697506148 | etot = -1077.76725732698
+4000  ekin = 123.015104309575 |  erot = 129.250631266888 | epot = -1330.03299290867 | etot = -1077.76725733221
+5000  ekin = 122.9570060981 |  erot = 129.822304188926 | epot = -1330.54656761964 | etot = -1077.76725733262
+6000  ekin = 122.758396503728 |  erot = 130.158463496347 | epot = -1330.68411732949 | etot = -1077.76725732941
+7000  ekin = 122.444997038107 |  erot = 130.2721351435 | epot = -1330.48438950495 | etot = -1077.76725732334
+8000  ekin = 122.055455926322 |  erot = 130.202756105441 | epot = -1330.02546934809 | etot = -1077.76725731633
+9000  ekin = 121.639778047767 |  erot = 130.001921534636 | epot = -1329.40895689073 | etot = -1077.76725730833
+10000  ekin = 121.255561480542 |  erot = 129.724613334693 | epot = -1328.74743211587 | etot = -1077.76725730064
+11000  ekin = 120.959150047792 |  erot = 129.417382591736 | epot = -1328.14378993383 | etot = -1077.7672572943
+12000  ekin = 120.804873255896 |  erot = 129.110119861451 | epot = -1327.68225040707 | etot = -1077.76725728973
+13000  ekin = 120.84692312026 |  erot = 128.811452781899 | epot = -1327.42563318933 | etot = -1077.76725728717
+14000  ekin = 121.124227416954 |  erot = 128.510318857508 | epot = -1327.40180356072 | etot = -1077.76725728626
+15000  ekin = 121.666723735015 |  erot = 128.179805529182 | epot = -1327.61378655278 | etot = -1077.76725728858
+16000  ekin = 122.48420413773 |  erot = 127.7714101238 | epot = -1328.02287155596 | etot = -1077.76725729443
+17000  ekin = 123.554901437623 |  erot = 127.223257664149 | epot = -1328.54541640317 | etot = -1077.7672573014
+18000  ekin = 124.838358543238 |  erot = 126.479155255363 | epot = -1329.0847711071 | etot = -1077.7672573085
+19000  ekin = 126.271030938727 |  erot = 125.497490625599 | epot = -1329.5357788797 | etot = -1077.76725731537
+20000  ekin = 127.785246119996 |  erot = 124.269691231027 | epot = -1329.82219466647 | etot = -1077.76725731544
+21000  ekin = 129.341920134184 |  erot = 122.835059904168 | epot = -1329.94423735083 | etot = -1077.76725731248
+22000  ekin = 130.919691006211 |  erot = 121.262876727301 | epot = -1329.94982504099 | etot = -1077.76725730747
+23000  ekin = 132.5067055481 |  erot = 119.63798200526 | epot = -1329.91194485558 | etot = -1077.76725730222
+24000  ekin = 134.092490326559 |  erot = 118.03901918442 | epot = -1329.8987668112 | etot = -1077.76725730022
+25000  ekin = 135.660464836621 |  erot = 116.515685186215 | epot = -1329.94340732287 | etot = -1077.76725730004
+26000  ekin = 137.186778726604 |  erot = 115.085213344397 | epot = -1330.03924937555 | etot = -1077.76725730455
+27000  ekin = 138.631216641226 |  erot = 113.733576310579 | epot = -1330.13205025948 | etot = -1077.76725730768
+28000  ekin = 139.956351860934 |  erot = 112.450817889846 | epot = -1330.17442705975 | etot = -1077.76725730897
+29000  ekin = 141.132095730945 |  erot = 111.248013058276 | epot = -1330.14736609674 | etot = -1077.76725730752
+30000  ekin = 142.135255524947 |  erot = 110.165318126416 | epot = -1330.06783095566 | etot = -1077.7672573043
+31000  ekin = 142.945319498095 |  erot = 109.26906345586 | epot = -1329.98164025322 | etot = -1077.76725729927
+32000  ekin = 143.550508334477 |  erot = 108.646435343349 | epot = -1329.96420097205 | etot = -1077.76725729422
+33000  ekin = 143.94192379333 |  erot = 108.385261854402 | epot = -1330.09444293819 | etot = -1077.76725729046
+34000  ekin = 144.112039801496 |  erot = 108.556164698166 | epot = -1330.43546178798 | etot = -1077.76725728832
+35000  ekin = 144.054908300964 |  erot = 109.203418763406 | epot = -1331.02558435228 | etot = -1077.76725728791
+36000  ekin = 143.757709793102 |  erot = 110.342536293123 | epot = -1331.86750337561 | etot = -1077.76725728938
+37000  ekin = 143.224204313506 |  erot = 111.95088434885 | epot = -1332.942345956 | etot = -1077.76725729365
+38000  ekin = 142.457513980673 |  erot = 113.968727530034 | epot = -1334.19349881072 | etot = -1077.76725730001
+39000  ekin = 141.463565854942 |  erot = 116.29723735485 | epot = -1335.52806051882 | etot = -1077.76725730903
+40000  ekin = 140.250124908962 |  erot = 118.793122406283 | epot = -1336.81050463699 | etot = -1077.76725732174
+41000  ekin = 138.820773211814 |  erot = 121.268568926308 | epot = -1337.85659947459 | etot = -1077.76725733647
+42000  ekin = 137.182796339923 |  erot = 123.506485031842 | epot = -1338.45653872253 | etot = -1077.76725735076
+43000  ekin = 135.367500581476 |  erot = 125.29033107441 | epot = -1338.42508901096 | etot = -1077.76725735508
+44000  ekin = 133.337269375167 |  erot = 126.415468495777 | epot = -1337.51999529678 | etot = -1077.76725742584
+45000  ekin = 131.439049413892 |  erot = 126.724836949372 | epot = -1335.93114371325 | etot = -1077.76725734999
+46000  ekin = 129.845441134595 |  erot = 126.391857491267 | epot = -1334.00455608503 | etot = -1077.76725745917
+47000  ekin = 128.256459545521 |  erot = 125.565939986762 | epot = -1331.58965689646 | etot = -1077.76725736418
+48000  ekin = 127.882214731217 |  erot = 124.234254983921 | epot = -1329.88372728254 | etot = -1077.76725756741
+49000  ekin = 127.351717354214 |  erot = 122.498251564086 | epot = -1327.61722629563 | etot = -1077.76725737733
+50000  ekin = 127.042187382637 |  erot = 120.712825414822 | epot = -1325.52227015942 | etot = -1077.76725736196
+51000  ekin = 126.939090812203 |  erot = 119.088171838498 | epot = -1323.7945200008 | etot = -1077.7672573501
+52000  ekin = 127.052758247807 |  erot = 117.797033031223 | epot = -1322.61704861958 | etot = -1077.76725734055
+53000  ekin = 127.367330865571 |  erot = 116.951027484839 | epot = -1322.08561579165 | etot = -1077.76725744124
+54000  ekin = 127.699598694243 |  erot = 116.588954946935 | epot = -1322.05581098738 | etot = -1077.7672573462
+55000  ekin = 128.765472970124 |  erot = 116.722527775949 | epot = -1323.25525818877 | etot = -1077.76725744269
+56000  ekin = 129.745971272492 |  erot = 117.329047803033 | epot = -1324.84227644251 | etot = -1077.76725736699
+57000  ekin = 130.68679923891 |  erot = 118.336149226794 | epot = -1326.79020584606 | etot = -1077.76725738035
+58000  ekin = 131.547485886187 |  erot = 119.658488175854 | epot = -1328.97323145072 | etot = -1077.76725738868
+59000  ekin = 132.288746551762 |  erot = 121.192124361468 | epot = -1331.2481283112 | etot = -1077.76725739797
+60000  ekin = 132.889658039575 |  erot = 122.813399448196 | epot = -1333.47031489469 | etot = -1077.76725740691
+61000  ekin = 133.34147638721 |  erot = 124.387402689362 | epot = -1335.49613649179 | etot = -1077.76725741522
+62000  ekin = 133.649114161524 |  erot = 125.778714754977 | epot = -1337.19508633847 | etot = -1077.76725742197
+63000  ekin = 133.82819881192 |  erot = 126.867080850077 | epot = -1338.46253708695 | etot = -1077.76725742496
+64000  ekin = 133.906684651824 |  erot = 127.563040672905 | epot = -1339.23698275248 | etot = -1077.76725742775
+65000  ekin = 133.909388287634 |  erot = 127.810288982225 | epot = -1339.48693469479 | etot = -1077.76725742493
+66000  ekin = 133.86081006735 |  erot = 127.603400400037 | epot = -1339.23146788818 | etot = -1077.76725742079
+67000  ekin = 133.775485591323 |  erot = 126.989915348575 | epot = -1338.53265835276 | etot = -1077.76725741286
+68000  ekin = 133.656407434476 |  erot = 126.056031307506 | epot = -1337.47969615099 | etot = -1077.76725740901
+69000  ekin = 133.498245523806 |  erot = 124.901121868324 | epot = -1336.16662479387 | etot = -1077.76725740175
+70000  ekin = 133.29399842671 |  erot = 123.635623442427 | epot = -1334.69687926337 | etot = -1077.76725739423
+71000  ekin = 133.029392386924 |  erot = 122.365171367186 | epot = -1333.16182114485 | etot = -1077.76725739074
+72000  ekin = 132.685056689193 |  erot = 121.171597639892 | epot = -1331.62391171537 | etot = -1077.76725738628
+73000  ekin = 132.251376493387 |  erot = 120.116099015078 | epot = -1330.13473289197 | etot = -1077.76725738351
+74000  ekin = 131.726574812548 |  erot = 119.247057316129 | epot = -1328.74088951045 | etot = -1077.76725738177
+75000  ekin = 131.110698166934 |  erot = 118.598252474103 | epot = -1327.47620801944 | etot = -1077.7672573784
+76000  ekin = 130.422389067205 |  erot = 118.195180955537 | epot = -1326.38482739773 | etot = -1077.76725737499
+77000  ekin = 129.697453900293 |  erot = 118.05495085627 | epot = -1325.51966212761 | etot = -1077.76725737104
+78000  ekin = 128.983808987508 |  erot = 118.189138027539 | epot = -1324.94020438318 | etot = -1077.76725736813
+79000  ekin = 128.33503884882 |  erot = 118.595476281743 | epot = -1324.69777249594 | etot = -1077.76725736537
+80000  ekin = 127.800117751073 |  erot = 119.26689064397 | epot = -1324.83426576002 | etot = -1077.76725736498
+81000  ekin = 127.407996010304 |  erot = 120.178391162382 | epot = -1325.35364454144 | etot = -1077.76725736875
+82000  ekin = 127.161473447285 |  erot = 121.280514709077 | epot = -1326.20924553086 | etot = -1077.76725737449
+83000  ekin = 127.04595184901 |  erot = 122.504106964497 | epot = -1327.31731619533 | etot = -1077.76725738182
+84000  ekin = 127.034443068044 |  erot = 123.770035256801 | epot = -1328.57173571383 | etot = -1077.76725738899
+85000  ekin = 127.100009803031 |  erot = 125.002871400657 | epot = -1329.87013859938 | etot = -1077.7672573957
+86000  ekin = 127.209916231691 |  erot = 126.126063406782 | epot = -1331.10323704296 | etot = -1077.76725740449
+87000  ekin = 127.33974310822 |  erot = 127.079810479666 | epot = -1332.186810994 | etot = -1077.76725740611
+88000  ekin = 127.492851572889 |  erot = 127.842496747421 | epot = -1333.1026057236 | etot = -1077.76725740329
+89000  ekin = 127.697668813164 |  erot = 128.428193060101 | epot = -1333.89311927022 | etot = -1077.76725739695
+90000  ekin = 128.002367682838 |  erot = 128.890624121692 | epot = -1334.66024919208 | etot = -1077.76725738755
+91000  ekin = 128.464258986688 |  erot = 129.314890049746 | epot = -1335.54640641371 | etot = -1077.76725737728
+92000  ekin = 129.138404881412 |  erot = 129.795965407416 | epot = -1336.70162765837 | etot = -1077.76725736954
+93000  ekin = 130.05988004796 |  erot = 130.410441748419 | epot = -1338.23757916353 | etot = -1077.76725736715
+94000  ekin = 131.22652253725 |  erot = 131.190635069448 | epot = -1340.18441497914 | etot = -1077.76725737244
+95000  ekin = 132.586213223046 |  erot = 132.107679404097 | epot = -1342.46115001118 | etot = -1077.76725738403
+96000  ekin = 134.044080427152 |  erot = 133.075735506149 | epot = -1344.8870733339 | etot = -1077.7672574006
+97000  ekin = 135.476028603552 |  erot = 133.967715320791 | epot = -1347.21100134248 | etot = -1077.76725741814
+98000  ekin = 136.748227204441 |  erot = 134.641388466874 | epot = -1349.15687309791 | etot = -1077.76725742659
+99000  ekin = 137.752624159367 |  erot = 134.99210077777 | epot = -1350.51198237554 | etot = -1077.7672574384
+100000  ekin = 138.392477025647 |  erot = 134.944608034508 | epot = -1351.10434250636 | etot = -1077.76725744621
+    100000   315.83543     -1390.6819      39.577599     -1212.7119     -0.012722464    6.1629505e+08
+Loop time of 85.2132 on 1 procs for 100000 steps with 148 atoms
+
+Performance: 1.730 ns/day, 13.875 hours/ns, 1173.528 timesteps/s, 173.682 katom-step/s
+99.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 81.71      | 81.71      | 81.71      |   0.0 | 95.89
+Bond    | 1.103      | 1.103      | 1.103      |   0.0 |  1.29
+Neigh   | 0.017589   | 0.017589   | 0.017589   |   0.0 |  0.02
+Comm    | 0.055508   | 0.055508   | 0.055508   |   0.0 |  0.07
+Output  | 0.1581     | 0.1581     | 0.1581     |   0.0 |  0.19
+Modify  | 2.0369     | 2.0369     | 2.0369     |   0.0 |  2.39
+Other   |            | 0.132      |            |       |  0.15
+
+Nlocal:            148 ave         148 max         148 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:           4199 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
+Neighbor list builds = 100
+Dangerous builds = 0
+
+write_data last_config.${number}.* nocoeff
+write_data last_config.5.* nocoeff
+System init for write_data ...
+Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
+#write_restart last_config.${number}.*
+Total wall time: 0:01:25

examples/PACKAGES/cgdna/examples/real_units/oxDNA2/dsring/log.22May24.dsring.g++.4

@@ -0,0 +1,286 @@
+LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified)
+# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19
+variable number	equal 5
+variable ofreq	equal 1000
+variable efreq	equal 1000
+variable T      equal 300.0
+variable rhos   equal 0.2
+
+units real
+
+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:132)
+atom_modify sort 0 8.518
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 17.036 bin
+neigh_modify every 1 delay 0 check yes
+
+read_data data.dsring
+Reading data file ...
+  orthogonal box = (0 0 0) to (851 851 851)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  148 atoms
+  reading velocities ...
+  148 velocities
+  scanning bonds ...
+  1 = max bonds/atom
+  148 ellipsoids
+  orthogonal box = (0 0 0) to (851 851 851)
+  1 by 2 by 2 MPI processor grid
+  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 = 0.015 seconds
+
+set atom * mass 315.8376
+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 * 11.92337812042065 2.1295 6.4430152
+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 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576
+pair_coeff * * oxdna2/stk seqdep ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/stk seqdep 300 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
+pair_coeff 1 4 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
+pair_coeff 2 3 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
+pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 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 4.80673207785863 3.4072 5.1108 1.87396 4.94044 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 300 ${rhos} 0.815
+pair_coeff * * oxdna2/dh 300 0.2 0.815
+
+# NVE ensemble
+fix 1 all nve/asphere
+#fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10
+
+timestep 0.01706
+
+#comm_style tiled
+fix 3 all balance 1000 1.03 shift xyz 10 1.03
+comm_modify cutoff 32.4
+
+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
+Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 48.032697
+  ghost atom cutoff = 48.032697
+  binsize = 24.016348, 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 48.03269686950012 (../comm.cpp:739)
+0  ekin = 122.015812851425 |  erot = 125.402528675609 | epot = -1325.18559882055 | etot = -1077.76725729351
+Per MPI rank memory allocation (min/avg/max) = 7.619 | 7.668 | 7.742 Mbytes
+   Step          Temp          E_pair         E_mol          TotEng         Press          Volume    
+         0   278.46107     -1367.7166      42.531022     -1203.1698     -0.0059756093   6.1629505e+08
+1000  ekin = 122.370905858635 |  erot = 126.447129514011 | epot = -1326.58529267981 | etot = -1077.76725730716
+2000  ekin = 122.691275133791 |  erot = 127.497291822808 | epot = -1327.95582427469 | etot = -1077.76725731809
+3000  ekin = 122.920677842253 |  erot = 128.459039892254 | epot = -1329.14697506148 | etot = -1077.76725732698
+4000  ekin = 123.015104309575 |  erot = 129.250631266888 | epot = -1330.03299290867 | etot = -1077.7672573322
+5000  ekin = 122.957006098101 |  erot = 129.822304188925 | epot = -1330.54656761964 | etot = -1077.76725733262
+6000  ekin = 122.758396503728 |  erot = 130.158463496346 | epot = -1330.68411732949 | etot = -1077.76725732941
+7000  ekin = 122.444997038108 |  erot = 130.272135143499 | epot = -1330.48438950495 | etot = -1077.76725732334
+8000  ekin = 122.055455926323 |  erot = 130.202756105441 | epot = -1330.02546934809 | etot = -1077.76725731633
+9000  ekin = 121.639778047767 |  erot = 130.001921534637 | epot = -1329.40895689073 | etot = -1077.76725730833
+10000  ekin = 121.255561480543 |  erot = 129.724613334694 | epot = -1328.74743211587 | etot = -1077.76725730063
+11000  ekin = 120.959150047793 |  erot = 129.417382591737 | epot = -1328.14378993382 | etot = -1077.76725729429
+12000  ekin = 120.804873255897 |  erot = 129.110119861453 | epot = -1327.68225040707 | etot = -1077.76725728972
+13000  ekin = 120.846923120261 |  erot = 128.8114527819 | epot = -1327.42563318933 | etot = -1077.76725728717
+14000  ekin = 121.124227416955 |  erot = 128.51031885751 | epot = -1327.40180356072 | etot = -1077.76725728625
+15000  ekin = 121.666723735015 |  erot = 128.179805529184 | epot = -1327.61378655278 | etot = -1077.76725728858
+16000  ekin = 122.48420413773 |  erot = 127.771410123803 | epot = -1328.02287155596 | etot = -1077.76725729443
+17000  ekin = 123.554901437623 |  erot = 127.223257664152 | epot = -1328.54541640317 | etot = -1077.76725730139
+18000  ekin = 124.838358543238 |  erot = 126.479155255366 | epot = -1329.0847711071 | etot = -1077.7672573085
+19000  ekin = 126.271030938727 |  erot = 125.497490625601 | epot = -1329.53577887969 | etot = -1077.76725731536
+20000  ekin = 127.785246119996 |  erot = 124.269691231029 | epot = -1329.82219466646 | etot = -1077.76725731543
+21000  ekin = 129.341920134184 |  erot = 122.835059904169 | epot = -1329.94423735083 | etot = -1077.76725731247
+22000  ekin = 130.91969100621 |  erot = 121.2628767273 | epot = -1329.94982504098 | etot = -1077.76725730747
+23000  ekin = 132.506705548099 |  erot = 119.637982005259 | epot = -1329.91194485557 | etot = -1077.76725730222
+24000  ekin = 134.092490326558 |  erot = 118.039019184419 | epot = -1329.89876681119 | etot = -1077.76725730022
+25000  ekin = 135.660464836621 |  erot = 116.515685186213 | epot = -1329.94340732286 | etot = -1077.76725730003
+26000  ekin = 137.186778726603 |  erot = 115.085213344396 | epot = -1330.03924937554 | etot = -1077.76725730454
+27000  ekin = 138.631216641226 |  erot = 113.733576310578 | epot = -1330.13205025948 | etot = -1077.76725730767
+28000  ekin = 139.956351860934 |  erot = 112.450817889845 | epot = -1330.17442705975 | etot = -1077.76725730897
+29000  ekin = 141.132095730946 |  erot = 111.248013058276 | epot = -1330.14736609673 | etot = -1077.76725730751
+30000  ekin = 142.135255524949 |  erot = 110.165318126416 | epot = -1330.06783095566 | etot = -1077.76725730429
+31000  ekin = 142.945319498097 |  erot = 109.269063455861 | epot = -1329.98164025322 | etot = -1077.76725729926
+32000  ekin = 143.550508334479 |  erot = 108.64643534335 | epot = -1329.96420097205 | etot = -1077.76725729422
+33000  ekin = 143.941923793332 |  erot = 108.385261854403 | epot = -1330.09444293819 | etot = -1077.76725729046
+34000  ekin = 144.112039801499 |  erot = 108.556164698166 | epot = -1330.43546178798 | etot = -1077.76725728831
+35000  ekin = 144.054908300967 |  erot = 109.203418763407 | epot = -1331.02558435228 | etot = -1077.76725728791
+36000  ekin = 143.757709793105 |  erot = 110.342536293123 | epot = -1331.8675033756 | etot = -1077.76725728938
+37000  ekin = 143.224204313509 |  erot = 111.950884348849 | epot = -1332.942345956 | etot = -1077.76725729364
+38000  ekin = 142.457513980675 |  erot = 113.968727530033 | epot = -1334.19349881072 | etot = -1077.76725730001
+39000  ekin = 141.463565854944 |  erot = 116.297237354849 | epot = -1335.52806051882 | etot = -1077.76725730903
+40000  ekin = 140.250124908963 |  erot = 118.793122406281 | epot = -1336.81050463698 | etot = -1077.76725732174
+41000  ekin = 138.820773211815 |  erot = 121.268568926305 | epot = -1337.85659947459 | etot = -1077.76725733647
+42000  ekin = 137.182796339923 |  erot = 123.506485031839 | epot = -1338.45653872252 | etot = -1077.76725735076
+43000  ekin = 135.367500581475 |  erot = 125.290331074407 | epot = -1338.42508901096 | etot = -1077.76725735507
+44000  ekin = 133.337269375166 |  erot = 126.415468495773 | epot = -1337.51999529677 | etot = -1077.76725742583
+45000  ekin = 131.43904941389 |  erot = 126.724836949369 | epot = -1335.93114371325 | etot = -1077.76725734999
+46000  ekin = 129.845441134593 |  erot = 126.391857491264 | epot = -1334.00455608502 | etot = -1077.76725745916
+47000  ekin = 128.256459545521 |  erot = 125.565939986761 | epot = -1331.58965689646 | etot = -1077.76725736417
+48000  ekin = 127.882214731216 |  erot = 124.23425498392 | epot = -1329.88372728254 | etot = -1077.7672575674
+49000  ekin = 127.351717354214 |  erot = 122.498251564087 | epot = -1327.61722629563 | etot = -1077.76725737733
+50000  ekin = 127.042187382636 |  erot = 120.712825414824 | epot = -1325.52227015942 | etot = -1077.76725736196
+51000  ekin = 126.939090812203 |  erot = 119.088171838501 | epot = -1323.7945200008 | etot = -1077.76725735009
+52000  ekin = 127.052758247806 |  erot = 117.797033031227 | epot = -1322.61704861958 | etot = -1077.76725734055
+53000  ekin = 127.36733086557 |  erot = 116.951027484844 | epot = -1322.08561579166 | etot = -1077.76725744124
+54000  ekin = 127.699598694242 |  erot = 116.588954946942 | epot = -1322.05581098738 | etot = -1077.7672573462
+55000  ekin = 128.765472970119 |  erot = 116.722527775956 | epot = -1323.25525818877 | etot = -1077.76725744269
+56000  ekin = 129.745971272485 |  erot = 117.329047803041 | epot = -1324.84227644252 | etot = -1077.76725736699
+57000  ekin = 130.686799238902 |  erot = 118.336149226803 | epot = -1326.79020584605 | etot = -1077.76725738035
+58000  ekin = 131.547485886178 |  erot = 119.658488175863 | epot = -1328.97323145072 | etot = -1077.76725738868
+59000  ekin = 132.288746551752 |  erot = 121.192124361476 | epot = -1331.24812831119 | etot = -1077.76725739797
+60000  ekin = 132.889658039566 |  erot = 122.813399448204 | epot = -1333.47031489469 | etot = -1077.76725740692
+61000  ekin = 133.341476387201 |  erot = 124.387402689369 | epot = -1335.49613649179 | etot = -1077.76725741522
+62000  ekin = 133.649114161516 |  erot = 125.778714754983 | epot = -1337.19508633847 | etot = -1077.76725742197
+63000  ekin = 133.828198811913 |  erot = 126.867080850083 | epot = -1338.46253708696 | etot = -1077.76725742496
+64000  ekin = 133.906684651817 |  erot = 127.56304067291 | epot = -1339.23698275248 | etot = -1077.76725742776
+65000  ekin = 133.909388287628 |  erot = 127.81028898223 | epot = -1339.48693469479 | etot = -1077.76725742493
+66000  ekin = 133.860810067346 |  erot = 127.603400400042 | epot = -1339.23146788819 | etot = -1077.7672574208
+67000  ekin = 133.775485591319 |  erot = 126.98991534858 | epot = -1338.53265835276 | etot = -1077.76725741286
+68000  ekin = 133.656407434473 |  erot = 126.056031307511 | epot = -1337.479696151 | etot = -1077.76725740901
+69000  ekin = 133.498245523803 |  erot = 124.901121868328 | epot = -1336.16662479388 | etot = -1077.76725740175
+70000  ekin = 133.293998426708 |  erot = 123.635623442431 | epot = -1334.69687926337 | etot = -1077.76725739423
+71000  ekin = 133.029392386922 |  erot = 122.36517136719 | epot = -1333.16182114486 | etot = -1077.76725739074
+72000  ekin = 132.685056689192 |  erot = 121.171597639896 | epot = -1331.62391171537 | etot = -1077.76725738628
+73000  ekin = 132.251376493386 |  erot = 120.116099015081 | epot = -1330.13473289197 | etot = -1077.76725738351
+74000  ekin = 131.726574812547 |  erot = 119.247057316132 | epot = -1328.74088951045 | etot = -1077.76725738177
+75000  ekin = 131.110698166933 |  erot = 118.598252474106 | epot = -1327.47620801944 | etot = -1077.7672573784
+76000  ekin = 130.422389067204 |  erot = 118.195180955539 | epot = -1326.38482739773 | etot = -1077.76725737499
+77000  ekin = 129.697453900292 |  erot = 118.054950856271 | epot = -1325.51966212761 | etot = -1077.76725737104
+78000  ekin = 128.983808987507 |  erot = 118.18913802754 | epot = -1324.94020438318 | etot = -1077.76725736813
+79000  ekin = 128.33503884882 |  erot = 118.595476281743 | epot = -1324.69777249594 | etot = -1077.76725736537
+80000  ekin = 127.800117751073 |  erot = 119.266890643969 | epot = -1324.83426576002 | etot = -1077.76725736498
+81000  ekin = 127.407996010304 |  erot = 120.178391162381 | epot = -1325.35364454144 | etot = -1077.76725736875
+82000  ekin = 127.161473447286 |  erot = 121.280514709075 | epot = -1326.20924553085 | etot = -1077.76725737449
+83000  ekin = 127.045951849011 |  erot = 122.504106964495 | epot = -1327.31731619533 | etot = -1077.76725738182
+84000  ekin = 127.034443068046 |  erot = 123.770035256799 | epot = -1328.57173571383 | etot = -1077.76725738899
+85000  ekin = 127.100009803033 |  erot = 125.002871400656 | epot = -1329.87013859939 | etot = -1077.7672573957
+86000  ekin = 127.209916231694 |  erot = 126.12606340678 | epot = -1331.10323704296 | etot = -1077.76725740449
+87000  ekin = 127.339743108223 |  erot = 127.079810479664 | epot = -1332.186810994 | etot = -1077.76725740611
+88000  ekin = 127.492851572892 |  erot = 127.842496747418 | epot = -1333.1026057236 | etot = -1077.76725740329
+89000  ekin = 127.697668813166 |  erot = 128.428193060097 | epot = -1333.89311927021 | etot = -1077.76725739695
+90000  ekin = 128.00236768284 |  erot = 128.890624121688 | epot = -1334.66024919208 | etot = -1077.76725738755
+91000  ekin = 128.464258986691 |  erot = 129.314890049742 | epot = -1335.54640641371 | etot = -1077.76725737728
+92000  ekin = 129.138404881414 |  erot = 129.795965407411 | epot = -1336.70162765836 | etot = -1077.76725736954
+93000  ekin = 130.059880047962 |  erot = 130.410441748414 | epot = -1338.23757916353 | etot = -1077.76725736715
+94000  ekin = 131.226522537251 |  erot = 131.190635069444 | epot = -1340.18441497913 | etot = -1077.76725737244
+95000  ekin = 132.586213223046 |  erot = 132.107679404094 | epot = -1342.46115001117 | etot = -1077.76725738403
+96000  ekin = 134.044080427153 |  erot = 133.075735506146 | epot = -1344.88707333389 | etot = -1077.76725740059
+97000  ekin = 135.476028603552 |  erot = 133.967715320788 | epot = -1347.21100134248 | etot = -1077.76725741814
+98000  ekin = 136.748227204441 |  erot = 134.641388466873 | epot = -1349.15687309791 | etot = -1077.76725742659
+99000  ekin = 137.752624159367 |  erot = 134.99210077777 | epot = -1350.51198237554 | etot = -1077.7672574384
+100000  ekin = 138.392477025646 |  erot = 134.94460803451 | epot = -1351.10434250636 | etot = -1077.76725744621
+    100000   315.83543     -1390.6819      39.577599     -1212.7119     -0.012722464    6.1629505e+08
+Loop time of 30.2255 on 4 procs for 100000 steps with 148 atoms
+
+Performance: 4.877 ns/day, 4.921 hours/ns, 3308.461 timesteps/s, 489.652 katom-step/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    | 16.766     | 22.691     | 26.962     |  89.3 | 75.07
+Bond    | 0.28821    | 0.30757    | 0.32075    |   2.3 |  1.02
+Neigh   | 0.008451   | 0.008527   | 0.008607   |   0.1 |  0.03
+Comm    | 2.0101     | 6.3007     | 12.277     | 170.6 | 20.85
+Output  | 0.051655   | 0.054646   | 0.056776   |   0.9 |  0.18
+Modify  | 0.53953    | 0.56983    | 0.63795    |   5.3 |  1.89
+Other   |            | 0.2934     |            |       |  0.97
+
+Nlocal:             37 ave          38 max          36 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Nghost:            111 ave         112 max         110 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Neighs:        1049.75 ave        1288 max         753 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
+Neighbor list builds = 100
+Dangerous builds = 0
+
+write_data last_config.${number}.* nocoeff
+write_data last_config.5.* nocoeff
+System init for write_data ...
+Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
+#write_restart last_config.${number}.*
+Total wall time: 0:00:30

examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex1/data.duplex1

@@ -0,0 +1,68 @@
+LAMMPS data file in real units via oxdna lj2real.py, date 2024-05-19
+
+10 atoms
+4 atom types
+8 bonds
+1 bond types
+10 ellipsoids
+
+-170 170 xlo xhi
+-170 170 ylo yhi
+-170 170 zlo zhi
+
+Masses
+
+1 315.8376
+2 315.8376
+3 315.8376
+4 315.8376
+
+Atoms # hybrid
+
+1 1 -2.8740969069282687 -3.723118600434732 5.494693518792015 1 1 1.0016462505133576 0 0 0
+2 2 -2.7379071878387986 -6.079929519421481 10.066032484018534 1 1 1.0016462505133576 0 0 0
+3 3 -1.110437385073819 -7.791537941948432 13.848676172779387 1 1 1.0016462505133576 0 0 0
+4 4 1.4306089998272526 -8.354886654263622 17.79828313773629 1 1 1.0016462505133576 0 0 0
+5 1 3.9498326729322186 -6.646891787969407 20.657842369456382 1 1 1.0016462505133576 0 0 0
+6 4 -3.801540967989063 0.7719150486872158 21.01300417274477 2 1 1.0016462505133576 0 0 0
+7 1 -0.287657468030243 1.787063409177335 17.702181979507532 2 1 1.0016462505133576 0 0 0
+8 2 2.8086617684512323 1.5040732709582532 14.656350509768911 2 1 1.0016462505133576 0 0 0
+9 3 5.165059071666839 0.3988634556159852 10.50699529001116 2 1 1.0016462505133576 0 0 0
+10 4 6.817789789050184 -3.1038996716078557 8.419212766646357 2 1 1.0016462505133576 0 0 0
+
+Velocities
+
+1 0.0015993537866009029 -0.000680681865016988 -0.00014678467473993874 1.3034875452014287 -0.6725260292370423 1.5263182328899618
+2 0.0008422431968202534 -0.0002471920411024751 0.0007894382186365997 -0.32615096872390803 -0.0034351199136194157 -0.9136220137417161
+3 -0.0011446153381118452 0.00041850425643063176 -0.00045926941555484915 1.7184317758530245 2.6050996986101502 -0.47065934236730145
+4 -0.0011077496385743138 0.0002472924939324634 -0.00034633314311123244 -0.5778245520276679 1.752085001878762 -0.24048635097513535
+5 0.0004072478403200556 -0.0012804934445473403 0.0008610591638760516 0.23142339993018143 0.3972766524238825 1.363641236078021
+6 0.00017968178785700138 -0.00024308968845109275 0.00014280408309295725 0.1704955558294103 -1.3525913126172677 1.5501424653239764
+7 -4.108556803115003e-05 0.00023724044475488887 -0.00013843701960263193 0.7809156374181498 -2.1218743676572576 0.2975087875146955
+8 -0.00035835254321313353 0.0008579277312926632 0.0019500603503724006 -0.711656157643413 -2.0351916264105014 -0.7613827970610736
+9 -0.0008730894357027041 -0.00039026927657647716 0.0002796967510539106 -1.193834703375802 1.023301140813147 -1.8342354268493246
+10 0.0009421885758929626 -0.0005326396944231774 0.0006296458639527654 -0.24420734152643714 1.5633648178267814 0.6376075187926279
+
+Bonds
+
+1 1 1 2
+2 1 2 3
+3 1 3 4
+4 1 4 5
+5 1 6 7
+6 1 7 8
+7 1 8 9
+8 1 9 10
+
+Ellipsoids
+
+1 9.999999997766462 9.999999997766462 9.999999997766462 0.9890278201757743 0.01779228232037064 -0.14337734159225404 0.030827642240801516
+2 9.999999997766462 9.999999997766462 9.999999997766462 0.939687458852748 0.04174166924055095 -0.023337773785056866 0.338674565089608
+3 9.999999997766462 9.999999997766462 9.999999997766462 0.8210113150655425 0.03012140921736572 0.017666019956944813 0.5698429897612057
+4 9.999999997766462 9.999999997766462 9.999999997766462 0.6623662858285051 -0.028186343967346823 0.022942552517501488 0.7482981175276918
+5 9.999999997766462 9.999999997766462 9.999999997766462 0.3601488726765216 0.0513614985821682 0.0724224158335286 0.9286602067807472
+6 9.999999997766462 9.999999997766462 9.999999997766462 0.11941234710084649 0.9244660117493703 -0.35317942248051865 -0.07979711784524246
+7 9.999999997766462 9.999999997766462 9.999999997766462 -0.17949125421205164 0.7412884899431119 -0.6379094464220707 0.1065166771202199
+8 9.999999997766462 9.999999997766462 9.999999997766462 -0.10483691088405202 0.5508895999584645 -0.8250090480220789 0.06992811634525403
+9 9.999999997766462 9.999999997766462 9.999999997766462 0.07777239911646 -0.3724087549185288 0.9103052384821374 -0.1631181963720798
+10 9.999999997766462 9.999999997766462 9.999999997766462 0.16279109707978262 0.027148630125149613 0.9849325709665359 -0.0516705065113425

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

@@ -0,0 +1,73 @@
+# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19
+variable number	equal 1
+variable ofreq	equal 1000
+variable efreq	equal 1000
+variable T      equal 300.0
+variable rhos   equal 0.2
+
+units real
+
+dimension 3
+
+newton on
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid oxdna
+atom_modify sort 0 8.518
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 17.036 bin
+neigh_modify every 1 delay 0 check yes
+
+read_data data.duplex1
+
+set atom * mass 315.8376
+
+group all type 1 4
+
+# oxDNA2 bond interactions - FENE backbone
+bond_style oxdna2/fene
+bond_coeff * 11.92337812042065 2.1295 6.4430152
+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 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576
+pair_coeff * * oxdna2/stk seqav ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/hbond seqav 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
+pair_coeff 1 4 oxdna2/hbond seqav 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
+pair_coeff 2 3 oxdna2/hbond seqav 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
+pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 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 4.80673207785863 3.4072 5.1108 1.87396 4.94044 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} 4265.0 457145 angmom 10
+
+timestep 0.01706
+
+#comm_style tiled
+fix 3 all balance 1000 1.03 shift xyz 10 1.03
+comm_modify cutoff 32.4
+
+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 1000000
+
+write_data last_config.${number}.* nocoeff
+#write_restart last_config.${number}.*

examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex2/data.duplex2

@@ -0,0 +1,91 @@
+LAMMPS data file in real units via oxdna lj2real.py, date 2024-05-19
+
+16 atoms
+4 atom types
+13 bonds
+1 bond types
+16 ellipsoids
+
+-170 170 xlo xhi
+-170 170 ylo yhi
+-170 170 zlo zhi
+
+Masses
+
+1 315.8376
+2 315.8376
+3 315.8376
+4 315.8376
+
+Atoms # hybrid
+
+1 1 -5.224492277936935 -5.6003990662830665 3.072035980595378 1 1 1.0016462505133576 0 0 0
+2 2 -3.855482258589815 -8.54410812515585 6.182955020430966 1 1 1.0016462505133576 0 0 0
+3 3 -0.8418698080395857 -10.56041032511679 9.10967975032824 1 1 1.0016462505133576 0 0 0
+4 4 2.502394065492512 -10.715431837829685 12.145744722571814 1 1 1.0016462505133576 0 0 0
+5 1 5.355178690564601 -8.674171903962998 15.067785212133312 1 1 1.0016462505133576 0 0 0
+6 2 6.7305169669220595 -5.763569949980494 18.347908888941284 1 1 1.0016462505133576 0 0 0
+7 3 6.061219006086631 -3.4238594469157198 21.88758604427721 1 1 1.0016462505133576 0 0 0
+8 4 4.001186577913306 -2.576839632838177 26.12300846270287 1 1 1.0016462505133576 0 0 0
+9 1 3.454997351061381 -12.298079702286948 26.05718083554597 2 1 1.0016462505133576 0 0 0
+10 2 -0.2728181587270111 -11.028698363238112 23.169872406755868 2 1 1.0016462505133576 0 0 0
+11 3 -2.692868178466912 -7.73787195036868 20.549852065183913 2 1 1.0016462505133576 0 0 0
+12 4 -3.316857346830113 -4.145374554885233 17.08862230448963 2 1 1.0016462505133576 0 0 0
+13 1 -0.5308965342198838 -0.6095451431748122 13.28229291571604 3 1 1.0016462505133576 0 0 0
+14 2 1.5233668194980015 -0.46991432454420656 8.699204689407908 3 1 1.0016462505133576 0 0 0
+15 3 3.844548159551531 -2.026909836907328 5.074452450044903 3 1 1.0016462505133576 0 0 0
+16 4 4.325141724684425 -4.740799489595668 1.4104749932020408 3 1 1.0016462505133576 0 0 0
+
+Velocities
+
+1 0.00026896558742537556 0.00011298695236274073 0.001242364337461123 0.7538466533118467 -1.2587520584415195 -1.1163576881067447
+2 -0.00019946914535880285 0.0013465785184092233 -0.0009479872206420321 -0.13024003640483983 -0.5006975787807386 0.17048535791572514
+3 -0.0010377647810347322 -0.0006804774738725614 -0.000302697462953215 -0.15638545864527348 -0.2683843524758034 -0.6295604792026762
+4 -0.0011968051721949484 -0.002808404437492725 0.00016214368951061121 -0.7029471277015998 1.2169631204234201 1.42700472482703
+5 -0.0008046113463391788 -0.001142874812754601 -0.0006767129075723855 0.304218367349499 -0.4005571162913614 0.5710347488390389
+6 -0.00023475461149269044 0.000959484075931813 0.0007283860029089665 0.3921776444343422 -2.399417440979843 0.3950910265578085
+7 0.0002545632912247854 -0.00019202725318668095 -0.0007112078778547229 1.4800522749729792 1.8058703404340948 -0.5778414965351256
+8 0.0018887377488028885 -0.0002473511615838234 0.0008120520191337178 0.18841278062652408 0.3347372075847072 -0.5408605905745774
+9 0.0002452564077667799 0.00020601300929708606 6.1033299095680186e-05 0.13966147753401867 -0.0005390290197378453 0.6635632318913824
+10 0.000968244047328249 0.0005529827424647325 -0.00020224034557198784 -0.7235582069719148 -1.9412262416735993 -1.289806869224333
+11 -0.0017543321990246556 -0.000939796984860897 0.0018048542648271923 -1.5775475529872025 -2.0891633737315023 0.40142307521789933
+12 -0.0005934853675296159 0.001116191652783757 4.626275649966328e-05 -1.200961814632207 0.4371811217355096 0.43287366246768927
+13 -0.0007222905985558083 -0.0005767904238661645 0.0006648020330562531 -1.084763819731394 1.1718860080947717 0.2470159472481526
+14 0.0002573730178578412 -0.00182797610679242 -0.00033107273492769625 -0.510496177490122 0.29118940603730814 0.9195837620128926
+15 -0.0010092903785878923 0.0011654195253227475 4.0609661125969864e-05 -0.723803934131871 0.07956576746268508 -1.1413793944128399
+16 -0.0009587558806876301 -0.0004046946607553641 -0.0002343452641922075 0.07373406158203998 -1.3986322243084912 0.4617216556119086
+
+Bonds
+
+1 1 1 2
+2 1 2 3
+3 1 3 4
+4 1 4 5
+5 1 5 6
+6 1 6 7
+7 1 7 8
+8 1 9 10
+9 1 10 11
+10 1 11 12
+11 1 13 14
+12 1 14 15
+13 1 15 16
+
+Ellipsoids
+
+1 9.999999997766462 9.999999997766462 9.999999997766462 0.9964752158482045 -0.053253555733239796 0.011391163807102514 -0.06380787090289707
+2 9.999999997766462 9.999999997766462 9.999999997766462 0.9369923833143513 0.11220716044648564 0.06732538499716349 0.3239168400846305
+3 9.999999997766462 9.999999997766462 9.999999997766462 0.797964932091827 0.14473096354527873 0.18374142699366386 0.5554673737937029
+4 9.999999997766462 9.999999997766462 9.999999997766462 0.5660864821344559 0.14688275499481052 0.09873742533340191 0.8051226439917721
+5 9.999999997766462 9.999999997766462 9.999999997766462 0.2533023785125306 0.12062313161679827 0.08583012223905846 0.9559922359911086
+6 9.999999997766462 9.999999997766462 9.999999997766462 -0.03855807343534716 0.08405913137017908 0.02236505169306371 0.9954632800204194
+7 9.999999997766462 9.999999997766462 9.999999997766462 -0.45592844330248017 0.1004550065061007 -0.052524745294758785 0.8827679181910482
+8 9.999999997766462 9.999999997766462 9.999999997766462 0.768021221540491 -0.009582139884533599 0.03658677589040892 -0.63930665074644
+9 9.999999997766462 9.999999997766462 9.999999997766462 -0.23299975754512345 0.688686395231341 0.6747873944883376 -0.12682324016841584
+10 9.999999997766462 9.999999997766462 9.999999997766462 -0.24662061871907232 0.8744456399178389 0.39370836087823996 -0.13970261209395163
+11 9.999999997766462 9.999999997766462 9.999999997766462 -0.087475900850909 0.977367602388229 0.14493549113095577 -0.12686307572668784
+12 9.999999997766462 9.999999997766462 9.999999997766462 -0.03181169300779214 0.9634374984140112 -0.2442360692534371 -0.10547485630879185
+13 9.999999997766462 9.999999997766462 9.999999997766462 -0.032786070696572266 0.7922941528811777 -0.6084214170523915 -0.03191282109962717
+14 9.999999997766462 9.999999997766462 9.999999997766462 0.047188686288341455 0.6316396208287698 -0.7737349519945348 0.011783095844627799
+15 9.999999997766462 9.999999997766462 9.999999997766462 -0.05869980642620335 -0.34229358203414423 0.9376740835056508 0.012519965878508689
+16 9.999999997766462 9.999999997766462 9.999999997766462 -0.08582818143150042 0.0008707732197394232 0.9939540921464659 -0.0684691735853161

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

@@ -0,0 +1,73 @@
+# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19
+variable number	equal 2
+variable ofreq	equal 1000
+variable efreq	equal 1000
+variable T      equal 300.0
+variable rhos   equal 0.2
+
+units real
+
+dimension 3
+
+newton on
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid oxdna
+atom_modify sort 0 8.518
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 17.036 bin
+neigh_modify every 1 delay 0 check yes
+
+read_data data.duplex2
+
+set atom * mass 315.8376
+
+group all type 1 4
+
+# oxDNA2 bond interactions - FENE backbone
+bond_style oxdna2/fene
+bond_coeff * 11.92337812042065 2.1295 6.4430152
+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 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576
+pair_coeff * * oxdna2/stk seqav ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/hbond seqav 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
+pair_coeff 1 4 oxdna2/hbond seqav 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
+pair_coeff 2 3 oxdna2/hbond seqav 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
+pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 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 4.80673207785863 3.4072 5.1108 1.87396 4.94044 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} 4265.0 457145 angmom 10
+
+timestep 0.01706
+
+#comm_style tiled
+fix 3 all balance 1000 1.03 shift xyz 10 1.03
+comm_modify cutoff 32.4
+
+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 1000000
+
+write_data last_config.${number}.* nocoeff
+#write_restart last_config.${number}.*

examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex3/data.duplex3

@@ -0,0 +1,68 @@
+LAMMPS data file in real units via oxdna lj2real.py, date 2024-05-19
+
+10 atoms
+4 atom types
+8 bonds
+1 bond types
+10 ellipsoids
+
+-170 170 xlo xhi
+-170 170 ylo yhi
+-170 170 zlo zhi
+
+Masses
+
+1 100.0278
+2 100.0278
+3 100.0278
+4 100.0278
+
+Atoms # hybrid
+
+1 1 -0.9600635673395586 -6.697372578532395 11.214288461530149 1 1 0.016231479325760585 0 0 0
+2 2 -1.371418484333729 -8.644426415489871 15.09830243650489 1 1 0.016231479325760585 0 0 0
+3 3 -0.6216529396853785 -10.27130427566052 18.871948109873205 1 1 0.016231479325760585 0 0 0
+4 4 1.779062937600471 -10.807909849707325 23.24831121047697 1 1 0.016231479325760585 0 0 0
+5 1 4.239477379859167 -10.116984578731293 26.59145222824391 1 1 0.016231479325760585 0 0 0
+6 4 -1.9327071764636017 -1.6150385295751968 26.477847842079502 2 1 0.016231479325760585 0 0 0
+7 1 -0.2983880618807194 -0.9579116659377174 23.010952595199885 2 1 0.016231479325760585 0 0 0
+8 2 2.1503419307040095 -0.31467499729662424 19.779605638337472 2 1 0.016231479325760585 0 0 0
+9 3 5.687077844288683 -1.6585607691903788 17.32600745817322 2 1 0.016231479325760585 0 0 0
+10 4 7.960942109870774 -4.424349635235229 15.853866095654556 2 1 0.016231479325760585 0 0 0
+
+Velocities
+
+1 0.003670260004547261 -0.001065537256202598 0.00019820771627082902 2.190783710921869 -2.4582417153465035 1.7715963770507672
+2 0.002291113608335764 0.0007728773438117204 0.002296672286413572 -0.40551125639613556 -0.12256940476096484 0.7114827747471555
+3 -0.0004997750377219465 -0.0006770677373491773 -0.0006775964298166731 2.179995735254803 3.7414175740175044 -1.7280709663891953
+4 -0.00015182185791796758 -4.553427726427798e-05 0.001445301171404135 -0.9443175316300753 1.9770932892489974 -0.3048781148297085
+5 0.00010888231798112065 -0.0017696699496284707 0.002217080679988605 -0.08456353584305179 0.035965271955914695 -0.7051030632137099
+6 0.0002936592731756661 -0.0011965505946877099 0.0004708407813130548 -0.7164699339101465 -1.1698888787077064 2.094408810880699
+7 -2.1364103955982793e-05 5.577692626680783e-05 -0.0005335687118188998 1.5034116933686936 -2.4596844236201743 0.7286296966602159
+8 -0.002835367576168593 -0.00028136761767332186 -0.0006160127733736687 -0.26771671594599533 -2.360332797207871 -1.6798429613010255
+9 0.00037413027551487407 0.001890740851504142 0.0005563994572100851 -1.512871512517161 -1.4691678195901636 -2.245351079807635
+10 -0.0024375187569690418 -0.000550577454043892 0.000971907386756427 0.4399243786321997 1.6207637079017971 1.0900899238856114
+
+Bonds
+
+1 1 1 2
+2 1 2 3
+3 1 3 4
+4 1 4 5
+5 1 6 7
+6 1 7 8
+7 1 8 9
+8 1 9 10
+
+Ellipsoids
+
+1 26.93628110931426 26.93628110931426 26.93628110931426 0.9824438652148015 -0.023183015026523597 -0.18238525095550406 0.031657854475291056
+2 26.93628110931426 26.93628110931426 26.93628110931426 0.9303156820429525 0.02962373336578937 -0.07607439157272995 0.3575581814380256
+3 26.93628110931426 26.93628110931426 26.93628110931426 0.7912072782182723 -0.043679545103099016 -0.05996218100443608 0.6070318583758278
+4 26.93628110931426 26.93628110931426 26.93628110931426 0.6531869542452552 -0.03659000162837596 0.004181596561545229 0.7563005281201641
+5 26.93628110931426 26.93628110931426 26.93628110931426 0.3249781771672557 0.06207197535108856 0.03689277251937633 0.9429608568635791
+6 26.93628110931426 26.93628110931426 26.93628110931426 0.08029535222204207 0.8726095530830543 -0.46831094470633033 -0.11309325067392484
+7 26.93628110931426 26.93628110931426 26.93628110931426 -0.1303991484205687 0.7764383491760718 -0.6081660772848121 0.10135864274905797
+8 26.93628110931426 26.93628110931426 26.93628110931426 -0.14971034142173664 0.5769499085020084 -0.7973230447846137 0.09482393688465168
+9 26.93628110931426 26.93628110931426 26.93628110931426 0.21130729744233523 -0.37917864508185584 0.8946270178621702 -0.10590221939385809
+10 26.93628110931426 26.93628110931426 26.93628110931426 0.34278400171414436 0.15185237372800306 0.9252984668160771 0.05712032974191834

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

@@ -0,0 +1,73 @@
+# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19
+variable number	equal 3
+variable ofreq	equal 1000
+variable efreq	equal 1000
+variable T      equal 300.0
+variable rhos   equal 0.2
+
+units real
+
+dimension 3
+
+newton on
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid oxdna
+atom_modify sort 0 8.518
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 17.036 bin
+neigh_modify every 1 delay 0 check yes
+
+read_data data.duplex3
+
+set atom * mass 100.0278
+
+group all type 1 4
+
+# oxDNA2 bond interactions - FENE backbone
+bond_style oxdna2/fene
+bond_coeff * 11.92337812042065 2.1295 6.4430152
+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 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576
+pair_coeff * * oxdna2/stk seqdep ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
+pair_coeff 1 4 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
+pair_coeff 2 3 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
+pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 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 4.80673207785863 3.4072 5.1108 1.87396 4.94044 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} 4265.0 457145 angmom 10
+
+timestep 0.01706
+
+#comm_style tiled
+fix 3 all balance 1000 1.03 shift xyz 10 1.03
+comm_modify cutoff 32.4
+
+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 1000000
+
+write_data last_config.${number}.* nocoeff
+#write_restart last_config.${number}.*

examples/PACKAGES/cgdna/examples/real_units/oxDNA2/potential_file/data.duplex1

@@ -0,0 +1,68 @@
+LAMMPS data file in real units via oxdna lj2real.py, date 2024-05-19
+
+10 atoms
+4 atom types
+8 bonds
+1 bond types
+10 ellipsoids
+
+-170 170 xlo xhi
+-170 170 ylo yhi
+-170 170 zlo zhi
+
+Masses
+
+1 315.8376
+2 315.8376
+3 315.8376
+4 315.8376
+
+Atoms # hybrid
+
+1 1 -2.8740969069282687 -3.723118600434732 5.494693518792015 1 1 1.0016462505133576 0 0 0
+2 2 -2.7379071878387986 -6.079929519421481 10.066032484018534 1 1 1.0016462505133576 0 0 0
+3 3 -1.110437385073819 -7.791537941948432 13.848676172779387 1 1 1.0016462505133576 0 0 0
+4 4 1.4306089998272526 -8.354886654263622 17.79828313773629 1 1 1.0016462505133576 0 0 0
+5 1 3.9498326729322186 -6.646891787969407 20.657842369456382 1 1 1.0016462505133576 0 0 0
+6 4 -3.801540967989063 0.7719150486872158 21.01300417274477 2 1 1.0016462505133576 0 0 0
+7 1 -0.287657468030243 1.787063409177335 17.702181979507532 2 1 1.0016462505133576 0 0 0
+8 2 2.8086617684512323 1.5040732709582532 14.656350509768911 2 1 1.0016462505133576 0 0 0
+9 3 5.165059071666839 0.3988634556159852 10.50699529001116 2 1 1.0016462505133576 0 0 0
+10 4 6.817789789050184 -3.1038996716078557 8.419212766646357 2 1 1.0016462505133576 0 0 0
+
+Velocities
+
+1 0.0015993537866009029 -0.000680681865016988 -0.00014678467473993874 1.3034875452014287 -0.6725260292370423 1.5263182328899618
+2 0.0008422431968202534 -0.0002471920411024751 0.0007894382186365997 -0.32615096872390803 -0.0034351199136194157 -0.9136220137417161
+3 -0.0011446153381118452 0.00041850425643063176 -0.00045926941555484915 1.7184317758530245 2.6050996986101502 -0.47065934236730145
+4 -0.0011077496385743138 0.0002472924939324634 -0.00034633314311123244 -0.5778245520276679 1.752085001878762 -0.24048635097513535
+5 0.0004072478403200556 -0.0012804934445473403 0.0008610591638760516 0.23142339993018143 0.3972766524238825 1.363641236078021
+6 0.00017968178785700138 -0.00024308968845109275 0.00014280408309295725 0.1704955558294103 -1.3525913126172677 1.5501424653239764
+7 -4.108556803115003e-05 0.00023724044475488887 -0.00013843701960263193 0.7809156374181498 -2.1218743676572576 0.2975087875146955
+8 -0.00035835254321313353 0.0008579277312926632 0.0019500603503724006 -0.711656157643413 -2.0351916264105014 -0.7613827970610736
+9 -0.0008730894357027041 -0.00039026927657647716 0.0002796967510539106 -1.193834703375802 1.023301140813147 -1.8342354268493246
+10 0.0009421885758929626 -0.0005326396944231774 0.0006296458639527654 -0.24420734152643714 1.5633648178267814 0.6376075187926279
+
+Bonds
+
+1 1 1 2
+2 1 2 3
+3 1 3 4
+4 1 4 5
+5 1 6 7
+6 1 7 8
+7 1 8 9
+8 1 9 10
+
+Ellipsoids
+
+1 9.999999997766462 9.999999997766462 9.999999997766462 0.9890278201757743 0.01779228232037064 -0.14337734159225404 0.030827642240801516
+2 9.999999997766462 9.999999997766462 9.999999997766462 0.939687458852748 0.04174166924055095 -0.023337773785056866 0.338674565089608
+3 9.999999997766462 9.999999997766462 9.999999997766462 0.8210113150655425 0.03012140921736572 0.017666019956944813 0.5698429897612057
+4 9.999999997766462 9.999999997766462 9.999999997766462 0.6623662858285051 -0.028186343967346823 0.022942552517501488 0.7482981175276918
+5 9.999999997766462 9.999999997766462 9.999999997766462 0.3601488726765216 0.0513614985821682 0.0724224158335286 0.9286602067807472
+6 9.999999997766462 9.999999997766462 9.999999997766462 0.11941234710084649 0.9244660117493703 -0.35317942248051865 -0.07979711784524246
+7 9.999999997766462 9.999999997766462 9.999999997766462 -0.17949125421205164 0.7412884899431119 -0.6379094464220707 0.1065166771202199
+8 9.999999997766462 9.999999997766462 9.999999997766462 -0.10483691088405202 0.5508895999584645 -0.8250090480220789 0.06992811634525403
+9 9.999999997766462 9.999999997766462 9.999999997766462 0.07777239911646 -0.3724087549185288 0.9103052384821374 -0.1631181963720798
+10 9.999999997766462 9.999999997766462 9.999999997766462 0.16279109707978262 0.027148630125149613 0.9849325709665359 -0.0516705065113425

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

@@ -0,0 +1,74 @@
+# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19
+variable number equal 1
+variable ofreq  equal 1000
+variable efreq  equal 1000
+variable T      equal 300.0
+variable rhos   equal 0.2
+
+units real
+
+dimension 3
+
+newton on
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid oxdna
+atom_modify sort 0 8.518
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 17.036 bin
+neigh_modify every 1 delay 0 check yes
+
+read_data data.duplex1
+
+set atom * mass 315.8376
+
+group all type 1 4
+
+# oxDNA2 bond interactions - FENE backbone
+bond_style oxdna2/fene
+bond_coeff * oxdna2_real.cgdna
+special_bonds fene
+
+# oxDNA2 pair interactions
+pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
+pair_coeff * * oxdna2/excv    oxdna2_real.cgdna
+pair_coeff * * oxdna2/stk     seqav 300.0 8.06199211612242 0.005309213 oxdna2_real.cgdna
+pair_coeff * * oxdna2/hbond   seqav oxdna2_real.cgdna
+pair_coeff 1 4 oxdna2/hbond   seqav oxdna2_real.cgdna
+pair_coeff 2 3 oxdna2/hbond   seqav oxdna2_real.cgdna
+pair_coeff * * oxdna2/xstk    oxdna2_real.cgdna
+pair_coeff * * oxdna2/coaxstk oxdna2_real.cgdna
+pair_coeff * * oxdna2/dh      300.0 0.5 oxdna2_real.cgdna
+
+
+# NVE ensemble
+fix 1 all nve/asphere
+#fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10
+
+timestep 0.01706
+
+#comm_style tiled
+fix 3 all balance 1000 1.03 shift xyz 10 1.03
+comm_modify cutoff 32.4
+
+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 1000000
+
+write_data last_config.${number}.* nocoeff
+#write_restart last_config.${number}.*

examples/PACKAGES/cgdna/examples/real_units/oxDNA2/potential_file/oxdna2_real.cgdna

@@ -0,0 +1 @@
+../../../../../../../potentials/oxdna2_real.cgdna

examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/data.duplex4.4type

@@ -0,0 +1,132 @@
+LAMMPS data file in real units via oxdna lj2real.py, date 2024-05-19
+
+26 atoms
+4 atom types
+24 bonds
+1 bond types
+26 ellipsoids
+
+-170 170 xlo xhi
+-170 170 ylo yhi
+-170 170 zlo zhi
+
+Masses
+
+1 315.8376
+2 315.8376
+3 315.8376
+4 315.8376
+
+Atoms # hybrid
+
+1 1 -5.088903454828145 -4.022006630398617 0.979450832492054 1 1 1.0016462505133576 0 0 0
+2 2 -3.073273348143933 -6.886121795405585 4.2637967191149935 1 1 1.0016462505133576 0 0 0
+3 3 -1.6015249052848957 -7.954971258517993 7.983259491779774 1 1 1.0016462505133576 0 0 0
+4 4 1.6004494372303046 -7.502206000462345 11.142183230976523 1 1 1.0016462505133576 0 0 0
+5 1 3.9762269824284777 -5.378694720128274 14.092706034736517 1 1 1.0016462505133576 0 0 0
+6 2 5.244098183685422 -2.0736999117014334 17.034635513902522 1 1 1.0016462505133576 0 0 0
+7 3 4.66434547759629 0.9057195140116471 20.406471315843888 1 1 1.0016462505133576 0 0 0
+8 4 3.3770131096003007 2.884613516099349 24.32212902640886 1 1 1.0016462505133576 0 0 0
+9 1 0.7795485088930724 2.8596780468864993 27.93316866219941 1 1 1.0016462505133576 0 0 0
+10 2 -2.220644638122167 1.9976911283301424 30.852747566202943 1 1 1.0016462505133576 0 0 0
+11 3 -3.752108563283866 -0.36118973532266224 34.56060757623137 1 1 1.0016462505133576 0 0 0
+12 4 -4.0981351277114095 -3.3336637232155737 38.03472139175804 1 1 1.0016462505133576 0 0 0
+13 1 -2.580860807366316 -5.296690457458744 41.65233354663661 1 1 1.0016462505133576 0 0 0
+14 4 3.11235736590125 3.9787921540654274 41.61858344700847 2 1 1.0016462505133576 0 0 0
+15 1 4.972174868431865 1.22026293032667 39.080053199424356 2 1 1.0016462505133576 0 0 0
+16 2 6.193349083696695 -1.843990009872412 35.70127548826449 2 1 1.0016462505133576 0 0 0
+17 3 4.85045978654294 -5.086115266816092 32.287814957190825 2 1 1.0016462505133576 0 0 0
+18 4 2.7413887948469777 -6.6667612407190076 28.945688671744993 2 1 1.0016462505133576 0 0 0
+19 1 0.23801913694460985 -6.962572452460229 24.638294488589953 2 1 1.0016462505133576 0 0 0
+20 2 -2.929295143505978 -5.793156995357843 22.155368377440084 2 1 1.0016462505133576 0 0 0
+21 3 -4.874287161624311 -2.6868984302083723 19.162406167006097 2 1 1.0016462505133576 0 0 0
+22 4 -4.466038023713098 -0.16009445500929992 14.199167217812603 2 1 1.0016462505133576 0 0 0
+23 1 -3.805032901797115 1.3047989425274054 9.939919176722297 2 1 1.0016462505133576 0 0 0
+24 2 -0.3645313828582167 2.0504253339486334 6.749830838323167 2 1 1.0016462505133576 0 0 0
+25 3 2.8696234661228 1.1843850873648512 3.5779840008575166 2 1 1.0016462505133576 0 0 0
+26 4 4.584052070339748 -2.4162961106383802 0.4178747538604132 2 1 1.0016462505133576 0 0 0
+
+Velocities
+
+1 -0.0007092826233374404 -0.0011683182237858898 0.0009345415878891811 -0.19711297351977997 0.3471662755040702 1.1876949496899232
+2 0.0001692806579311005 0.001454411904318072 -0.0009132068521112497 0.40085230919108755 -0.18887849087800404 0.047091827325408245
+3 0.00026721094548725233 -0.0018474107413693995 -7.33687581476124e-05 0.46267958346439353 1.0098887515959383 0.6393407481151142
+4 0.0005530692647148845 6.276724836348722e-05 0.0011760622369354724 0.485473149019376 -1.016731064060453 0.4763136256195711
+5 0.0010959077967915062 -0.002073578927849095 0.0009200279724368436 1.0623586979165884 1.065939836735458 -1.5037672467577814
+6 -0.0011992989214254961 -0.0008200232774176946 -1.878586889584186e-05 0.2637939462292815 0.9503989065450423 -1.6260870297579495
+7 0.0006177535901987009 0.000518919774167013 0.0003998839732602718 -0.6408171281169938 0.36348341926995353 -1.375803360797847
+8 0.00016059142531900045 -0.0006450606532728585 0.0008669204672450051 -0.7477778258878353 0.47361246994539824 -0.5810846842200627
+9 8.231216517048786e-05 6.015188190262039e-05 6.125792756154739e-05 -0.4607197796707098 0.5637456934375974 0.26087415190460156
+10 -0.000500147138046807 -0.000463066044342822 0.000355851169196805 -0.36328886676626787 -0.43369687106567045 0.5273136714151697
+11 0.0007757175683907118 -8.926233267161596e-05 -0.0008385947169209714 -0.4808110547195639 0.46086842856246785 -1.2339214306000716
+12 -0.001263650191118318 0.00028219137594863816 -0.0014126973797773772 0.3775783079049196 -0.1807429862945671 2.0452684483124046
+13 -3.2579866050976174e-05 0.0002635521160422669 0.0004611578260851882 -0.7261457161482728 -0.9102614938022983 -0.950223070000176
+14 -0.0004505866261683952 0.0009690259297353478 -0.0013620790360894626 0.7053189033188233 0.2384556381419323 0.771670025066328
+15 0.0011631309106043411 0.00044570587091719976 8.76640977124226e-05 0.6336939456886027 0.23680623944908769 0.16348552253269122
+16 -6.374073980270027e-05 -0.0002931008886831666 0.001121388312515121 -0.22078626344978855 0.4828157321900567 -1.5155692478249987
+17 -0.0010186027342478764 -0.002155869929612435 -0.0002602846290421834 -0.7045426361887308 -0.35130535920917716 -1.3344634305851248
+18 0.0013185658893551267 2.047723112341404e-05 -0.0005696586063762746 -1.6060222297755182 0.09031942024852611 0.9877781291576422
+19 -0.0014036986693625635 0.0012719382904391608 1.897600955961397e-05 0.9208051089916969 -1.6695360996503725 0.9680334678576618
+20 -0.0017040889747209288 0.00025337668854442876 -0.0001691840039087206 -0.5820811149791364 -0.6584676155867104 -0.13895286467266474
+21 -0.0012832301288169161 0.00023432762658239688 0.0004175391014650396 -0.368479743293301 -0.13070387294699928 -0.7972536298008709
+22 0.000425865764618422 0.0005323528439718917 -0.00037084207215630813 -1.987484231007066 -0.8187640783546725 0.8567029127863278
+23 -0.0004662057261624694 -0.0009522140435800978 0.0009625566807134454 0.07570418552326717 -1.5530387610102858 1.0623583182518839
+24 -0.0008020353772621954 0.0006130763545177365 0.000256600283460346 -0.4133480645752746 -1.123177366593782 0.34895664453469977
+25 -0.0007357778484794694 0.0004842720240985607 -0.0010361169830474496 0.23875324331203535 -0.5925750420871833 0.1484289925046781
+26 -0.000301663155222858 0.001775092432198598 -0.0009822913284976214 0.0628202961121918 0.11750852756815655 -0.8762490863383418
+
+Bonds
+
+1 1 1 2
+2 1 2 3
+3 1 3 4
+4 1 4 5
+5 1 5 6
+6 1 6 7
+7 1 7 8
+8 1 8 9
+9 1 9 10
+10 1 10 11
+11 1 11 12
+12 1 12 13
+13 1 14 15
+14 1 15 16
+15 1 16 17
+16 1 17 18
+17 1 18 19
+18 1 19 20
+19 1 20 21
+20 1 21 22
+21 1 22 23
+22 1 23 24
+23 1 24 25
+24 1 25 26
+
+Ellipsoids
+
+1 9.999999997766462 9.999999997766462 9.999999997766462 0.9970278940278272 0.0014876174054512252 0.0750547523448584 0.017319055267040844
+2 9.999999997766462 9.999999997766462 9.999999997766462 0.9059171712388804 0.007913225291438054 0.04634256838354512 0.42083705406683053
+3 9.999999997766462 9.999999997766462 9.999999997766462 0.7657426991864452 0.028071560533125216 0.13224385975981257 0.6287779160305484
+4 9.999999997766462 9.999999997766462 9.999999997766462 0.5238981696613685 0.0516703526741727 0.1609645534282743 0.8348360887142046
+5 9.999999997766462 9.999999997766462 9.999999997766462 0.30973290897949424 0.0750672191209306 0.23962885621884192 0.9170651279902646
+6 9.999999997766462 9.999999997766462 9.999999997766462 -0.050269263744563454 0.08142241031464711 0.09584085715741358 0.9907865170259763
+7 9.999999997766462 9.999999997766462 9.999999997766462 -0.3805122714271814 0.08965734720629535 0.057827749665601925 0.9186010683391725
+8 9.999999997766462 9.999999997766462 9.999999997766462 -0.6066322463100545 0.015286960797006149 0.035984536832974555 0.7940206166563465
+9 9.999999997766462 9.999999997766462 9.999999997766462 0.771660293819677 0.02607541526374929 -0.08047223278265907 -0.6303845520092687
+10 9.999999997766462 9.999999997766462 9.999999997766462 0.9119628434851113 0.03686258000931541 -0.11017000132786052 -0.3934812487336936
+11 9.999999997766462 9.999999997766462 9.999999997766462 0.9917294290821066 0.05835078551401739 -0.08073737536574405 -0.08092837290732445
+12 9.999999997766462 9.999999997766462 9.999999997766462 0.9763527785523285 0.06753089597617556 0.004847281702108697 0.205307899901351
+13 9.999999997766462 9.999999997766462 9.999999997766462 0.8553397145502984 0.1399133966151149 0.07233200118835512 0.49354462388392356
+14 9.999999997766462 9.999999997766462 9.999999997766462 0.014416326682630282 -0.533642571147991 0.8442695396252617 0.04718813669228716
+15 9.999999997766462 9.999999997766462 9.999999997766462 0.14095892784917538 -0.2201285495070387 0.9406003462562982 -0.21666792788520955
+16 9.999999997766462 9.999999997766462 9.999999997766462 0.07323967796304806 0.05035907488974361 0.963136526452943 -0.2539053850556888
+17 9.999999997766462 9.999999997766462 9.999999997766462 0.030254986187638885 0.39195467212588947 0.9164794947567249 -0.07430684019611289
+18 9.999999997766462 9.999999997766462 9.999999997766462 -0.03080283760241768 0.6526511470205414 0.7481495879677094 -0.11562810865943304
+19 9.999999997766462 9.999999997766462 9.999999997766462 -0.09450197979153381 0.7469150592813072 0.6556128255138505 -0.0579576833217777
+20 9.999999997766462 9.999999997766462 9.999999997766462 -0.12903334341475137 0.9222523214328698 0.3501336268694509 -0.10103214950765672
+21 9.999999997766462 9.999999997766462 9.999999997766462 -0.0069954457806870336 0.9888131084284681 -0.09413955816471489 -0.11548785185859346
+22 9.999999997766462 9.999999997766462 9.999999997766462 0.029336230851923526 0.9805894852440379 -0.19236800606724952 -0.02404573205262194
+23 9.999999997766462 9.999999997766462 9.999999997766462 0.03080980270092377 0.872234086776475 -0.4869211139732921 0.03415088124407873
+24 9.999999997766462 9.999999997766462 9.999999997766462 0.007237815450514786 0.690265186998662 -0.7210993183911308 0.05913847022922672
+25 9.999999997766462 9.999999997766462 9.999999997766462 0.06694683426684143 -0.46894411325316443 0.8712038661029582 -0.12889283810247346
+26 9.999999997766462 9.999999997766462 9.999999997766462 0.07581973147109407 -0.10215114654759445 0.9759556607577902 -0.17699451916228467

examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/data.duplex4.8type

@@ -0,0 +1,136 @@
+LAMMPS data file in real units via oxdna lj2real.py, date 2024-05-19
+
+26 atoms
+8 atom types
+24 bonds
+1 bond types
+26 ellipsoids
+
+-170 170 xlo xhi
+-170 170 ylo yhi
+-170 170 zlo zhi
+
+Masses
+
+1 315.8376
+2 315.8376
+3 315.8376
+4 315.8376
+5 315.8376
+6 315.8376
+7 315.8376
+8 315.8376
+
+Atoms # hybrid
+
+1 1 -5.088903454828145 -4.022006630398617 0.979450832492054 1 1 1.0016462505133576 0 0 0
+2 2 -3.073273348143933 -6.886121795405585 4.2637967191149935 1 1 1.0016462505133576 0 0 0
+3 3 -1.6015249052848957 -7.954971258517993 7.983259491779774 1 1 1.0016462505133576 0 0 0
+4 4 1.6004494372303046 -7.502206000462345 11.142183230976523 1 1 1.0016462505133576 0 0 0
+5 5 3.9762269824284777 -5.378694720128274 14.092706034736517 1 1 1.0016462505133576 0 0 0
+6 6 5.244098183685422 -2.0736999117014334 17.034635513902522 1 1 1.0016462505133576 0 0 0
+7 7 4.66434547759629 0.9057195140116471 20.406471315843888 1 1 1.0016462505133576 0 0 0
+8 8 3.3770131096003007 2.884613516099349 24.32212902640886 1 1 1.0016462505133576 0 0 0
+9 1 0.7795485088930724 2.8596780468864993 27.93316866219941 1 1 1.0016462505133576 0 0 0
+10 2 -2.220644638122167 1.9976911283301424 30.852747566202943 1 1 1.0016462505133576 0 0 0
+11 7 -3.752108563283866 -0.36118973532266224 34.56060757623137 1 1 1.0016462505133576 0 0 0
+12 8 -4.0981351277114095 -3.3336637232155737 38.03472139175804 1 1 1.0016462505133576 0 0 0
+13 1 -2.580860807366316 -5.296690457458744 41.65233354663661 1 1 1.0016462505133576 0 0 0
+14 4 3.11235736590125 3.9787921540654274 41.61858344700847 2 1 1.0016462505133576 0 0 0
+15 5 4.972174868431865 1.22026293032667 39.080053199424356 2 1 1.0016462505133576 0 0 0
+16 6 6.193349083696695 -1.843990009872412 35.70127548826449 2 1 1.0016462505133576 0 0 0
+17 3 4.85045978654294 -5.086115266816092 32.287814957190825 2 1 1.0016462505133576 0 0 0
+18 4 2.7413887948469777 -6.6667612407190076 28.945688671744993 2 1 1.0016462505133576 0 0 0
+19 5 0.23801913694460985 -6.962572452460229 24.638294488589953 2 1 1.0016462505133576 0 0 0
+20 6 -2.929295143505978 -5.793156995357843 22.155368377440084 2 1 1.0016462505133576 0 0 0
+21 7 -4.874287161624311 -2.6868984302083723 19.162406167006097 2 1 1.0016462505133576 0 0 0
+22 8 -4.466038023713098 -0.16009445500929992 14.199167217812603 2 1 1.0016462505133576 0 0 0
+23 1 -3.805032901797115 1.3047989425274054 9.939919176722297 2 1 1.0016462505133576 0 0 0
+24 2 -0.3645313828582167 2.0504253339486334 6.749830838323167 2 1 1.0016462505133576 0 0 0
+25 3 2.8696234661228 1.1843850873648512 3.5779840008575166 2 1 1.0016462505133576 0 0 0
+26 4 4.584052070339748 -2.4162961106383802 0.4178747538604132 2 1 1.0016462505133576 0 0 0
+
+Velocities
+
+1 -0.0007092826233374404 -0.0011683182237858898 0.0009345415878891811 -0.19711297351977997 0.3471662755040702 1.1876949496899232
+2 0.0001692806579311005 0.001454411904318072 -0.0009132068521112497 0.40085230919108755 -0.18887849087800404 0.047091827325408245
+3 0.00026721094548725233 -0.0018474107413693995 -7.33687581476124e-05 0.46267958346439353 1.0098887515959383 0.6393407481151142
+4 0.0005530692647148845 6.276724836348722e-05 0.0011760622369354724 0.485473149019376 -1.016731064060453 0.4763136256195711
+5 0.0010959077967915062 -0.002073578927849095 0.0009200279724368436 1.0623586979165884 1.065939836735458 -1.5037672467577814
+6 -0.0011992989214254961 -0.0008200232774176946 -1.878586889584186e-05 0.2637939462292815 0.9503989065450423 -1.6260870297579495
+7 0.0006177535901987009 0.000518919774167013 0.0003998839732602718 -0.6408171281169938 0.36348341926995353 -1.375803360797847
+8 0.00016059142531900045 -0.0006450606532728585 0.0008669204672450051 -0.7477778258878353 0.47361246994539824 -0.5810846842200627
+9 8.231216517048786e-05 6.015188190262039e-05 6.125792756154739e-05 -0.4607197796707098 0.5637456934375974 0.26087415190460156
+10 -0.000500147138046807 -0.000463066044342822 0.000355851169196805 -0.36328886676626787 -0.43369687106567045 0.5273136714151697
+11 0.0007757175683907118 -8.926233267161596e-05 -0.0008385947169209714 -0.4808110547195639 0.46086842856246785 -1.2339214306000716
+12 -0.001263650191118318 0.00028219137594863816 -0.0014126973797773772 0.3775783079049196 -0.1807429862945671 2.0452684483124046
+13 -3.2579866050976174e-05 0.0002635521160422669 0.0004611578260851882 -0.7261457161482728 -0.9102614938022983 -0.950223070000176
+14 -0.0004505866261683952 0.0009690259297353478 -0.0013620790360894626 0.7053189033188233 0.2384556381419323 0.771670025066328
+15 0.0011631309106043411 0.00044570587091719976 8.76640977124226e-05 0.6336939456886027 0.23680623944908769 0.16348552253269122
+16 -6.374073980270027e-05 -0.0002931008886831666 0.001121388312515121 -0.22078626344978855 0.4828157321900567 -1.5155692478249987
+17 -0.0010186027342478764 -0.002155869929612435 -0.0002602846290421834 -0.7045426361887308 -0.35130535920917716 -1.3344634305851248
+18 0.0013185658893551267 2.047723112341404e-05 -0.0005696586063762746 -1.6060222297755182 0.09031942024852611 0.9877781291576422
+19 -0.0014036986693625635 0.0012719382904391608 1.897600955961397e-05 0.9208051089916969 -1.6695360996503725 0.9680334678576618
+20 -0.0017040889747209288 0.00025337668854442876 -0.0001691840039087206 -0.5820811149791364 -0.6584676155867104 -0.13895286467266474
+21 -0.0012832301288169161 0.00023432762658239688 0.0004175391014650396 -0.368479743293301 -0.13070387294699928 -0.7972536298008709
+22 0.000425865764618422 0.0005323528439718917 -0.00037084207215630813 -1.987484231007066 -0.8187640783546725 0.8567029127863278
+23 -0.0004662057261624694 -0.0009522140435800978 0.0009625566807134454 0.07570418552326717 -1.5530387610102858 1.0623583182518839
+24 -0.0008020353772621954 0.0006130763545177365 0.000256600283460346 -0.4133480645752746 -1.123177366593782 0.34895664453469977
+25 -0.0007357778484794694 0.0004842720240985607 -0.0010361169830474496 0.23875324331203535 -0.5925750420871833 0.1484289925046781
+26 -0.000301663155222858 0.001775092432198598 -0.0009822913284976214 0.0628202961121918 0.11750852756815655 -0.8762490863383418
+
+Bonds
+
+1 1 1 2
+2 1 2 3
+3 1 3 4
+4 1 4 5
+5 1 5 6
+6 1 6 7
+7 1 7 8
+8 1 8 9
+9 1 9 10
+10 1 10 11
+11 1 11 12
+12 1 12 13
+13 1 14 15
+14 1 15 16
+15 1 16 17
+16 1 17 18
+17 1 18 19
+18 1 19 20
+19 1 20 21
+20 1 21 22
+21 1 22 23
+22 1 23 24
+23 1 24 25
+24 1 25 26
+
+Ellipsoids
+
+1 9.999999997766462 9.999999997766462 9.999999997766462 0.9970278940278272 0.0014876174054512252 0.0750547523448584 0.017319055267040844
+2 9.999999997766462 9.999999997766462 9.999999997766462 0.9059171712388804 0.007913225291438054 0.04634256838354512 0.42083705406683053
+3 9.999999997766462 9.999999997766462 9.999999997766462 0.7657426991864452 0.028071560533125216 0.13224385975981257 0.6287779160305484
+4 9.999999997766462 9.999999997766462 9.999999997766462 0.5238981696613685 0.0516703526741727 0.1609645534282743 0.8348360887142046
+5 9.999999997766462 9.999999997766462 9.999999997766462 0.30973290897949424 0.0750672191209306 0.23962885621884192 0.9170651279902646
+6 9.999999997766462 9.999999997766462 9.999999997766462 -0.050269263744563454 0.08142241031464711 0.09584085715741358 0.9907865170259763
+7 9.999999997766462 9.999999997766462 9.999999997766462 -0.3805122714271814 0.08965734720629535 0.057827749665601925 0.9186010683391725
+8 9.999999997766462 9.999999997766462 9.999999997766462 -0.6066322463100545 0.015286960797006149 0.035984536832974555 0.7940206166563465
+9 9.999999997766462 9.999999997766462 9.999999997766462 0.771660293819677 0.02607541526374929 -0.08047223278265907 -0.6303845520092687
+10 9.999999997766462 9.999999997766462 9.999999997766462 0.9119628434851113 0.03686258000931541 -0.11017000132786052 -0.3934812487336936
+11 9.999999997766462 9.999999997766462 9.999999997766462 0.9917294290821066 0.05835078551401739 -0.08073737536574405 -0.08092837290732445
+12 9.999999997766462 9.999999997766462 9.999999997766462 0.9763527785523285 0.06753089597617556 0.004847281702108697 0.205307899901351
+13 9.999999997766462 9.999999997766462 9.999999997766462 0.8553397145502984 0.1399133966151149 0.07233200118835512 0.49354462388392356
+14 9.999999997766462 9.999999997766462 9.999999997766462 0.014416326682630282 -0.533642571147991 0.8442695396252617 0.04718813669228716
+15 9.999999997766462 9.999999997766462 9.999999997766462 0.14095892784917538 -0.2201285495070387 0.9406003462562982 -0.21666792788520955
+16 9.999999997766462 9.999999997766462 9.999999997766462 0.07323967796304806 0.05035907488974361 0.963136526452943 -0.2539053850556888
+17 9.999999997766462 9.999999997766462 9.999999997766462 0.030254986187638885 0.39195467212588947 0.9164794947567249 -0.07430684019611289
+18 9.999999997766462 9.999999997766462 9.999999997766462 -0.03080283760241768 0.6526511470205414 0.7481495879677094 -0.11562810865943304
+19 9.999999997766462 9.999999997766462 9.999999997766462 -0.09450197979153381 0.7469150592813072 0.6556128255138505 -0.0579576833217777
+20 9.999999997766462 9.999999997766462 9.999999997766462 -0.12903334341475137 0.9222523214328698 0.3501336268694509 -0.10103214950765672
+21 9.999999997766462 9.999999997766462 9.999999997766462 -0.0069954457806870336 0.9888131084284681 -0.09413955816471489 -0.11548785185859346
+22 9.999999997766462 9.999999997766462 9.999999997766462 0.029336230851923526 0.9805894852440379 -0.19236800606724952 -0.02404573205262194
+23 9.999999997766462 9.999999997766462 9.999999997766462 0.03080980270092377 0.872234086776475 -0.4869211139732921 0.03415088124407873
+24 9.999999997766462 9.999999997766462 9.999999997766462 0.007237815450514786 0.690265186998662 -0.7210993183911308 0.05913847022922672
+25 9.999999997766462 9.999999997766462 9.999999997766462 0.06694683426684143 -0.46894411325316443 0.8712038661029582 -0.12889283810247346
+26 9.999999997766462 9.999999997766462 9.999999997766462 0.07581973147109407 -0.10215114654759445 0.9759556607577902 -0.17699451916228467

examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/generate_unique.py

@@ -0,0 +1,828 @@
+#!/usr/bin/env python
+"""
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/ Sandia National Laboratories
+   LAMMPS Development team: developers@lammps.org
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
+------------------------------------------------------------------------- */
+"""
+"""
+Creates unique base-pairings to avoid asymmetrical H-bonds.  
+
+Modified to create the bead wall setup.
+N_BEADS is the number of beads along one direction, the final system will have N_BEADS^2 beads in the wall. N_BEADS should be set to be odd number.
+"""
+
+
+#Define number of base-pairs per turn for B-form DNA
+N = 10.5
+#Define distance between the big bead and the centre of mass of the last base-pair
+BEAD_OFFSET = 2.0
+WALL_PARTICLE_SIZE = 2.0
+N_BEADS = 11
+
+#Number of unique base type groups (1-4) ACGT counts as one group
+N_BASE_TYPES = 20
+
+
+"""
+Import basic modules
+"""
+import sys, os, timeit
+
+from timeit import default_timer as timer
+start_time = timer()
+"""
+Try to import numpy; if failed, import a local version mynumpy 
+which needs to be provided
+"""
+try:
+    import numpy as np
+except:
+    print("numpy not found. Exiting.", file=sys.stderr)
+    sys.exit(1)
+
+"""
+Check that the required arguments (box offset and size in simulation units 
+and the sequence file were provided
+"""
+try:
+    box_offset = float(sys.argv[1])
+    box_length = float(sys.argv[2])
+    infile = sys.argv[3]
+    if len(sys.argv) == 4:
+        topo = 'strand'
+        lk = 0
+    elif len(sys.argv) == 5:
+        topo = 'strand'
+        lk = int(sys.argv[4])
+           
+except:
+    print("Usage: %s <%s> <%s> <%s> <%s> " % (sys.argv[0], \
+	"box offset", "box length", "file with sequences", "[Lk]"), file=sys.stderr)
+    sys.exit(1)
+box = np.array ([box_length, box_length, box_length])
+
+"""
+Try to open the file and fail gracefully if file cannot be opened
+"""
+try:
+    inp = open (infile, 'r')
+    inp.close()
+except:
+    print("Could not open file '%s' for reading. \
+					      Aborting." % infile, file=sys.stderr)
+    sys.exit(2)
+
+# return parts of a string
+def partition(s, d):
+    if d in s:
+        sp = s.split(d, 1)
+        return sp[0], d, sp[1]
+    else:
+        return s, "", ""
+
+"""
+Define the model constants
+"""
+# set model constants
+PI = np.pi
+POS_BASE =  0.4
+POS_BACK = -0.4
+EXCL_RC1 =  0.711879214356
+EXCL_RC2 =  0.335388426126
+EXCL_RC3 =  0.52329943261
+
+"""
+Define auxiliary variables for the construction of a helix
+"""
+# center of the double strand
+COM_CENTRE_DS = POS_BASE + 0.2
+
+# ideal rise between two consecutive nucleotides on the
+# same strand which are to be base paired in a duplex
+BASE_BASE = 0.3897628551303122
+
+# cutoff distance for overlap check
+RC2 = 16
+
+# squares of the excluded volume distances for overlap check
+RC2_BACK = EXCL_RC1**2
+RC2_BASE = EXCL_RC2**2
+RC2_BACK_BASE = EXCL_RC3**2
+
+# enumeration to translate from letters to numbers and vice versa
+number_to_base = {1 : 'A', 2 : 'C', 3 : 'G', 4 : 'T'}
+base_to_number = {'A' : 1, 'a' : 1, 'C' : 2, 'c' : 2,
+                  'G' : 3, 'g' : 3, 'T' : 4, 't' : 4}
+
+# auxiliary arrays
+positions = []
+a1s = []
+a3s = []
+quaternions = []
+
+newpositions = []
+newa1s = []
+newa3s = []
+
+basetype  = []
+strandnum = []
+
+bonds = []
+
+""" 
+Convert local body frame to quaternion DOF
+"""
+def exyz_to_quat (mya1, mya3):
+
+    mya2 = np.cross(mya3, mya1)
+    myquat = [1,0,0,0]
+
+    q0sq = 0.25 * (mya1[0] + mya2[1] + mya3[2] + 1.0)
+    q1sq = q0sq - 0.5 * (mya2[1] + mya3[2])
+    q2sq = q0sq - 0.5 * (mya1[0] + mya3[2])
+    q3sq = q0sq - 0.5 * (mya1[0] + mya2[1])
+
+    # some component must be greater than 1/4 since they sum to 1
+    # compute other components from it
+
+    if q0sq >= 0.25:
+        myquat[0] = np.sqrt(q0sq)
+        myquat[1] = (mya2[2] - mya3[1]) / (4.0*myquat[0])
+        myquat[2] = (mya3[0] - mya1[2]) / (4.0*myquat[0])
+        myquat[3] = (mya1[1] - mya2[0]) / (4.0*myquat[0])
+    elif q1sq >= 0.25:
+        myquat[1] = np.sqrt(q1sq)
+        myquat[0] = (mya2[2] - mya3[1]) / (4.0*myquat[1])
+        myquat[2] = (mya2[0] + mya1[1]) / (4.0*myquat[1])
+        myquat[3] = (mya1[2] + mya3[0]) / (4.0*myquat[1])
+    elif q2sq >= 0.25:
+        myquat[2] = np.sqrt(q2sq)
+        myquat[0] = (mya3[0] - mya1[2]) / (4.0*myquat[2])
+        myquat[1] = (mya2[0] + mya1[1]) / (4.0*myquat[2])
+        myquat[3] = (mya3[1] + mya2[2]) / (4.0*myquat[2])
+    elif q3sq >= 0.25:
+        myquat[3] = np.sqrt(q3sq)
+        myquat[0] = (mya1[1] - mya2[0]) / (4.0*myquat[3])
+        myquat[1] = (mya3[0] + mya1[2]) / (4.0*myquat[3])
+        myquat[2] = (mya3[1] + mya2[2]) / (4.0*myquat[3])
+
+    norm = 1.0/np.sqrt(myquat[0]*myquat[0] + myquat[1]*myquat[1] + \
+			  myquat[2]*myquat[2] + myquat[3]*myquat[3])
+    myquat[0] *= norm
+    myquat[1] *= norm
+    myquat[2] *= norm
+    myquat[3] *= norm
+
+    return np.array([myquat[0],myquat[1],myquat[2],myquat[3]])
+
+"""
+Adds a strand to the system by appending it to the array of previous strands
+"""
+def add_strands (mynewpositions, mynewa1s, mynewa3s):
+    overlap = False
+	
+    # This is a simple check for each of the particles where for previously 
+    # placed particles i we check whether it overlaps with any of the 
+    # newly created particles j
+
+    print("## Checking for overlaps", file=sys.stdout)
+
+    for i in range(len(positions)):
+
+        p = positions[i]
+        pa1 = a1s[i]
+
+        for j in range (len(mynewpositions)):
+
+            q = mynewpositions[j]
+            qa1 = mynewa1s[j]
+
+            # skip particles that are anyway too far away
+            dr = p - q
+            dr -= box * np.rint (dr / box)
+            if np.dot(dr, dr) > RC2:
+                continue
+
+            # base site and backbone site of the two particles
+            p_pos_back = p + pa1 * POS_BACK
+            p_pos_base = p + pa1 * POS_BASE
+            q_pos_back = q + qa1 * POS_BACK
+            q_pos_base = q + qa1 * POS_BASE
+
+            # check for no overlap between the two backbone sites
+            dr = p_pos_back - q_pos_back
+            dr -= box * np.rint (dr / box)
+            if np.dot(dr, dr) < RC2_BACK:
+                overlap = True
+
+            # check for no overlap between the two base sites
+            dr = p_pos_base -  q_pos_base
+            dr -= box * np.rint (dr / box)
+            if np.dot(dr, dr) < RC2_BASE:
+                overlap = True
+
+            # check for no overlap between backbone site of particle p 
+            # with base site of particle q
+            dr = p_pos_back - q_pos_base
+            dr -= box * np.rint (dr / box)
+            if np.dot(dr, dr) < RC2_BACK_BASE:
+                overlap = True
+
+            # check for no overlap between base site of particle p and 
+            # backbone site of particle q
+            dr = p_pos_base - q_pos_back
+            dr -= box * np.rint (dr / box)
+            if np.dot(dr, dr) < RC2_BACK_BASE:
+                overlap = True
+
+            # exit if there is an overlap
+            if overlap:
+                return False
+
+    # append to the existing list if no overlap is found
+    if not overlap:
+
+        for p in mynewpositions:
+            positions.append(p)
+        for p in mynewa1s:
+            a1s.append (p)
+        for p in mynewa3s:
+            a3s.append (p)
+	# calculate quaternion from local body frame and append
+        for ia in range(len(mynewpositions)):
+            mynewquaternions = exyz_to_quat(mynewa1s[ia],mynewa3s[ia])
+            quaternions.append(mynewquaternions)
+
+    return True
+
+"""
+Calculate angle of rotation site to site
+"""
+def get_angle(bp):
+   #n, minimal number of bases per turn
+   n = 10.5
+   found = False
+   while found == False:
+       turns = bp/n
+       diff = abs( turns - round(turns))
+       if diff < 0.03:
+           found = True
+           turns = round(turns)+lk
+           angle = (360*turns)/bp
+           angle = round (angle,2)
+           #angle =round( 360/n,2)
+       elif n > 11.5:
+           angle = 35.9
+           found = True
+       else:
+           n += 0.02
+   return angle
+
+
+def get_angle2(bp):
+    turns = bp/N + lk
+    angle = (360*turns)/bp
+    
+    return angle
+
+    
+
+"""
+Returns the rotation matrix defined by an axis and angle
+"""
+def get_rotation_matrix(axis, anglest, nbp=0):
+    # The argument anglest can be either an angle in radiants
+    # (accepted types are float, int or np.float64 or np.float64)
+    # or a tuple [angle, units] where angle is a number and
+    # units is a string. It tells the routine whether to use degrees,
+    # radiants (the default) or base pairs turns.
+    if not isinstance (anglest, (np.float64, np.float32, float, int)):
+        if len(anglest) > 1:
+            if anglest[1] in ["degrees", "deg", "o"]:
+                angle = (np.pi / 180.) * (anglest[0])
+            elif anglest[1] in ["bp"]:
+                if nbp == 0:
+                    angle = int(anglest[0]) * (np.pi / 180.) * (35.9)
+                else:    
+                    ang = get_angle2(nbp)
+                    angle = int(anglest[0]) * (np.pi / 180.) * (ang)
+            else:
+                angle = float(anglest[0])
+        else:
+            angle = float(anglest[0])
+    else:
+        angle = float(anglest) # in degrees (?)
+
+    axis = np.array(axis)
+    axis /= np.sqrt(np.dot(axis, axis))
+
+    ct = np.cos(angle)
+    st = np.sin(angle)
+    olc = 1. - ct
+    x, y, z = axis
+
+    return np.array([[olc*x*x+ct, olc*x*y-st*z, olc*x*z+st*y],
+                    [olc*x*y+st*z, olc*y*y+ct, olc*y*z-st*x],
+                    [olc*x*z-st*y, olc*y*z+st*x, olc*z*z+ct]])
+
+"""
+Generates the position and orientation vectors of a 
+(single or double) strand from a sequence string
+"""
+def generate_strand(bp, sequence=None, start_pos=np.array([0, 0, 0]), \
+	  dir=np.array([0, 0, 1]), perp=False, double=True, rot=0.):
+    # generate empty arrays
+    mynewpositions, mynewa1s, mynewa3s = [], [], []
+
+    # cast the provided start_pos array into a numpy array
+    start_pos = np.array(start_pos, dtype=float)
+
+    # overall direction of the helix
+    dir = np.array(dir, dtype=float)
+    #if sequence == None:
+    #    sequence = np.random.randint(1, 5, bp)
+
+    # the elseif here is most likely redundant 
+    #elif len(sequence) != bp:
+    #    n = bp - len(sequence)
+    #    sequence += np.random.randint(1, 5, n)
+    #    print("sequence is too short, adding %d random bases" % n, file=sys.stderr)
+
+    # normalize direction
+    dir_norm = np.sqrt(np.dot(dir,dir))
+    if dir_norm < 1e-10:
+        print("direction must be a valid vector,\
+                defaulting to (0, 0, 1)", file=sys.stderr)
+        dir = np.array([0, 0, 1])
+    else: dir /= dir_norm
+
+    # find a vector orthogonal to dir to act as helix direction,
+    # if not provided switch off random orientation
+    if perp is None or perp is False:
+        v1 = np.random.random_sample(3)
+        # comment in to suppress randomized base vector
+        v1 = [1,0,0]
+        v1 -= dir * (np.dot(dir, v1))
+        v1 /= np.sqrt(sum(v1*v1))
+    else:
+        v1 = perp;
+
+    # generate rotational matrix representing the overall rotation of the helix
+    R0 = get_rotation_matrix(dir, rot)
+	    
+    # rotation matrix corresponding to one step along the helix
+    R = get_rotation_matrix(dir, [1, "bp"],bp)
+
+    # set the vector a1 (backbone to base) to v1 
+    a1 = v1
+    
+    # apply the global rotation to a1 
+    a1 = np.dot(R0, a1)
+    
+    # set the position of the fist backbone site to start_pos
+    rb = np.array(start_pos)
+	    
+    # set a3 to the direction of the helix
+    a3 = dir
+
+    for i in range(bp):
+    # work out the position of the centre of mass of the nucleotide
+        rcom = rb - COM_CENTRE_DS * a1
+
+        # append to newpositions
+        mynewpositions.append(rcom)
+        mynewa1s.append(a1)
+        mynewa3s.append(a3)
+
+        # if we are not at the end of the helix, we work out a1 and rb for the 
+        # next nucleotide along the helix
+        if i != bp - 1:
+            a1 = np.dot(R, a1)
+            rb += a3 * BASE_BASE
+
+    # if we are working on a double strand, we do a cycle similar 
+    # to the previous one but backwards
+    if double == True:
+        a1 = -a1
+        a3 = -dir
+        R = R.transpose()
+        for i in range(bp):
+            rcom = rb - COM_CENTRE_DS * a1
+            mynewpositions.append (rcom)
+            mynewa1s.append (a1)
+            mynewa3s.append (a3)
+            a1 = np.dot(R, a1)
+            rb += a3 * BASE_BASE
+    
+  
+    #Calculate the positions of the bead wall
+    
+    last_base1 = mynewpositions[int( len(mynewpositions)/2 - 1) ]
+    last_base2 = mynewpositions[int( len(mynewpositions)/2) ]
+    mid_point =  (last_base1 + last_base2) / 2 
+    
+    NN = N_BEADS**2
+    p1 = [mid_point[0] - (N_BEADS-1)*WALL_PARTICLE_SIZE, mid_point[1] - (N_BEADS-1)*WALL_PARTICLE_SIZE, mid_point[2] + BEAD_OFFSET ]
+    for i in range(N_BEADS):
+        for j in range(N_BEADS):
+            position = [ p1[0] + 2*i*WALL_PARTICLE_SIZE, p1[1] + 2*j*WALL_PARTICLE_SIZE, p1[2]]
+            mynewa1s.append([1,0,0])
+            mynewa3s.append([1,0,0])
+            mynewpositions.append(position)
+
+    assert (len (mynewpositions) > 0)
+
+    return [mynewpositions, mynewa1s, mynewa3s]
+
+
+
+"""
+Main function for this script.
+Reads a text file with the following format:
+- Each line contains the sequence for a single strand (A,C,G,T)
+- Lines beginning with the keyword 'DOUBLE' produce double-stranded DNA
+
+Ex: Two ssDNA (single stranded DNA)
+ATATATA
+GCGCGCG
+
+Ex: Two strands, one double stranded, the other single stranded.
+DOUBLE AGGGCT
+CCTGTA
+
+"""
+
+def read_strands(filename):
+    try:
+        infile = open (filename)
+    except:
+        print("Could not open file '%s'. Aborting." % filename, file=sys.stderr)
+        sys.exit(2)
+
+    # This block works out the number of nucleotides and strands by reading 
+    # the number of non-empty lines in the input file and the number of letters,
+    # taking the possible DOUBLE keyword into account.
+    nstrands, nnucl, nbonds = 0, 0, 0
+    lines = infile.readlines()
+    for line in lines:
+        line = line.upper().strip()
+        if len(line) == 0:
+            continue
+        if line[:6] == 'DOUBLE':
+            line = line.split()[1]
+            length = len(line)
+            print("## Found duplex of %i base pairs" % length, file=sys.stdout)
+            nnucl += 2*length
+            nstrands += 2
+            nbonds+= 2*length
+            
+        else:
+            line = line.split()[0]
+            length = len(line)
+            print("## Found single strand of %i bases" % length, file=sys.stdout)
+            nnucl += length
+            nstrands += 1
+            if topo == 'ring':
+                nbonds =+ length
+            else:
+                nbonds += length+1
+    # rewind the sequence input file
+    infile.seek(0)
+
+    print("## nstrands, nnucl = ", nstrands, nnucl, file=sys.stdout)
+
+    # generate the data file in LAMMPS format
+    try:
+        out = open ("data.oxdna", "w")
+    except:
+        print("Could not open data file for writing. Aborting.", file=sys.stderr)
+        sys.exit(2)
+	
+    lines = infile.readlines()
+    nlines = len(lines)
+    i = 1
+    myns = 0
+    noffset = 1
+
+    for line in lines:
+        line = line.upper().strip()
+
+        # skip empty lines
+        if len(line) == 0: 
+            i += 1
+            continue
+
+	# block for duplexes: last argument of the generate function 
+	# is set to 'True'
+        if line[:6] == 'DOUBLE':
+            line = line.split()[1]
+            length = len(line)
+            seq = [(base_to_number[x]) for x in line]
+            seq = np.array(seq,dtype=int)
+            n_a, n_c, n_g, n_t = 0, 0, 0, 0
+            for s in range(seq.size):
+                if seq[s] == 1:
+                    n_a += 1
+                elif seq[s] == 2:
+                    n_c += 1
+                elif seq[s] ==3:
+                    n_g += 1
+                elif seq[s] == 4:
+                    n_t += 1
+            smallest_n_bases = n_c
+            if n_a < n_c:
+                smallest_n_bases = n_a
+            if smallest_n_bases > n_t:
+                smallest_n_bases = n_t
+            if smallest_n_bases > n_g:
+                smallest_n_bases = n_g
+             
+            if smallest_n_bases < N_BASE_TYPES:
+                print('## Not enough occurrences of base types in the sequence for ' + str(N_BASE_TYPES))
+                print('## unique base types, switching to ' + str(smallest_n_bases) + ' unique types')
+            else:
+                smallest_n_bases = N_BASE_TYPES
+           
+            a, c, g, t = -3, -2, -1, 0
+            for s in range(seq.size):
+                if seq[s] == 1: 
+                    if a < (smallest_n_bases*4-3):
+                        a += 4
+                    else:
+                        a = 1
+                    seq[s] = a
+                
+                elif seq[s] == 2: 
+                    if c < (smallest_n_bases*4-2):
+                        c += 4
+                    else:
+                        c = 2
+                    seq[s] = c
+
+                elif seq[s] == 3:
+                    if g < (smallest_n_bases*4-1):
+                        g += 4
+                    else:
+                        g = 3
+                    seq[s] = g
+                elif seq[s] == 4:
+                    if t < (smallest_n_bases*4):
+                        t += 4
+                    else:
+                        t = 4
+                    seq[s] = t
+                
+
+
+            myns += 1
+
+            for b in range(length):
+                basetype.append(seq[b])
+                strandnum.append(myns)
+
+            for b in range(length-1):
+                bondpair = [noffset + b, noffset + b + 1]
+                bonds.append(bondpair)
+     
+            
+            noffset += length 
+
+            # create the sequence of the second strand as made of 
+            # complementary bases
+            #seq2 = [5-s for s in seq]
+            seq2 = seq
+            for s in range(seq2.size):
+                if seq2[s]%4 == 1:
+                    seq2[s] += 3
+                elif seq2[s]%4 == 2:
+                    seq2[s] += 1
+                elif seq2[s]%4 == 3:
+                    seq2[s] -= 1
+                elif seq2[s]%4 == 0:
+                    seq2[s] -= 3    
+
+            #seq2.reverse()
+
+            myns += 1
+
+            for b in range(length):
+                basetype.append(seq2[b])
+                strandnum.append(myns)
+
+            for b in range(length-1):
+                bondpair = [noffset + b, noffset + b + 1]
+                bonds.append(bondpair)
+
+                     
+            #create wall bead types
+            bead_type = 4*smallest_n_bases + 1
+            for i in range(N_BEADS**2):
+                
+                basetype.append(bead_type)
+                basetype.append(bead_type)
+                strandnum.append(bead_type)
+                strandnum.append(bead_type)
+            #bonds.append([length, noffset + length])
+            #bonds.append([length+1, noffset + length])
+
+            noffset += length
+
+            print("## Created duplex of %i bases" % (2*length), file=sys.stdout)
+
+            # generate random position of the first nucleotide
+            com = box_offset + np.random.random_sample(3) * box
+            # comment out to randomize
+            com = [0,0,0]
+
+            # generate the random direction of the helix 
+            axis = np.random.random_sample(3)
+            # comment out to randomize
+            axis = [0,0,1]
+            axis /= np.sqrt(np.dot(axis, axis))
+
+            # use the generate function defined above to create 
+            # the position and orientation vector of the strand
+            if topo == 'ring':
+                newpositions, newa1s, newa3s = generate_ring(len(line), \
+                      sequence=seq, dir=axis, start_pos=com, double=True)
+            else:
+                newpositions, newa1s, newa3s = generate_strand(len(line), \
+                    sequence=seq, dir=axis, start_pos=com, double=True)
+
+            # generate a new position for the strand until it does not overlap
+            # with anything already present
+            start = timer()
+            while not add_strands(newpositions, newa1s, newa3s):
+                com = box_offset + np.random.random_sample(3) * box
+                axis = np.random.random_sample(3)
+                axis /= np.sqrt(np.dot(axis, axis))
+                if topo == 'ring':
+                    newpositions, newa1s, newa3s = generate_ring(len(line), \
+                        sequence=seq, dir=axis, start_pos=com, double=True)
+                else:
+                    newpositions, newa1s, newa3s = generate_strand(len(line), \
+                        sequence=seq, dir=axis, start_pos=com, double=True)
+                print("## Trying %i" % i, file=sys.stdout)
+            end = timer()
+            print("## Added duplex of %i bases (line %i/%i) in %.2fs, now at %i/%i" % \
+                          (2*length, i, nlines, end-start, len(positions), nnucl), file=sys.stdout)
+
+	# block for single strands: last argument of the generate function 
+	# is set to 'False'
+        else:
+            length = len(line)
+            seq = [(base_to_number[x]) for x in line]
+
+            myns += 1
+            for b in range(length):
+                basetype.append(seq[b])
+                strandnum.append(myns)
+
+            for b in range(length-1):
+                bondpair = [noffset + b, noffset + b + 1]
+                bonds.append(bondpair)
+            if topo == 'ring':    
+                bondpair = [noffset, noffset + length-1]
+                bonds.append(bondpair)
+            noffset += length
+            
+
+	    # generate random position of the first nucleotide
+            com = box_offset + np.random.random_sample(3) * box
+            # comment out to randomize
+            com = [-30,0,0]
+
+            # generate the random direction of the helix 
+            axis = np.random.random_sample(3)
+            # comment out to randomize
+            axis = [0,0,1]
+            axis /= np.sqrt(np.dot(axis, axis))
+
+            print("## Created single strand of %i bases" % length, file=sys.stdout)
+            if topo == 'ring':    
+                newpositions, newa1s, newa3s = generate_ring(length, \
+		              sequence=seq, dir=axis, start_pos=com, double=False)
+            else:
+                newpositions, newa1s, newa3s = generate_strand(length, \
+		               sequence=seq, dir=axis, start_pos=com, double=False)
+            start = timer()
+            while not add_strands(newpositions, newa1s, newa3s):
+                com = box_offset + np.random.random_sample(3) * box
+                axis = np.random.random_sample(3)
+                axis /= np.sqrt(np.dot(axis, axis))
+                if topo == 'ring':
+                    newpositions, newa1s, newa3s = generate_ring(length, \
+                          sequence=seq, dir=axis, start_pos=com, double=False)
+
+                else:    
+                    newpositions, newa1s, newa3s = generate_strand(length, \
+                          sequence=seq, dir=axis, start_pos=com, double=False)
+                print("## Trying  %i" % (i), file=sys.stdout)
+            end = timer()
+            print("## Added single strand of %i bases (line %i/%i) in %.2fs, now at %i/%i" % \
+				      (length, i, nlines, end-start,len(positions), nnucl), file=sys.stdout)
+
+        i += 1
+
+    # sanity check
+    #if not len(positions) == nnucl:
+    #    print(len(positions), nnucl)
+    #    raise AssertionError
+    nnucl = nnucl + (N_BEADS**2)
+    nbonds -= 4
+	
+    out.write('# LAMMPS data file\n')
+    out.write('%d atoms\n' % nnucl)
+    out.write('%d ellipsoids\n' % nnucl)
+    out.write('%d bonds\n' % nbonds)
+    out.write('\n')
+    out.write('%d atom types\n' %bead_type )
+    out.write('1 bond types\n')
+    out.write('\n')
+    out.write('# System size\n')
+    out.write('%f %f xlo xhi\n' % (box_offset,box_offset+box_length))
+    out.write('%f %f ylo yhi\n' % (box_offset,box_offset+box_length))
+    out.write('%f %f zlo zhi\n' % (0,box_length))
+
+    #out.write('\n')
+    #out.write('Masses\n')
+    #out.write('\n')
+    #out.write('1 3.1575\n')
+    #out.write('2 3.1575\n')
+    #out.write('3 3.1575\n')
+    #out.write('4 3.1575\n')
+    #out.write('5 3.1575\n')
+
+    # for each nucleotide print a line under the headers
+    # Atoms, Velocities, Ellipsoids and Bonds
+    out.write('\n')
+    out.write(\
+      '# Atom-ID, type, position, molecule-ID, ellipsoid flag, density\n')
+    out.write('Atoms\n')
+    out.write('\n')
+    
+    for i in range(nnucl):
+        out.write('%d %d %22.15le %22.15le %22.15le %d 1 1\n' \
+                  % (i+1, basetype[i], \
+                     positions[i][0], positions[i][1], positions[i][2], \
+                     strandnum[i]))
+
+    out.write('\n')
+    out.write('# Atom-ID, translational, rotational velocity\n')
+    out.write('Velocities\n')
+    out.write('\n')
+
+    for i in range(nnucl):
+        out.write("%d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le\n" \
+                  % (i+1,0.0,0.0,0.0,0.0,0.0,0.0))
+
+    out.write('\n')
+    out.write('# Atom-ID, shape, quaternion\n')
+    out.write('Ellipsoids\n')
+    out.write('\n')
+
+    for i in range(nnucl):
+        out.write(\
+    "%d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le\n"  \
+      % (i+1,1.1739845031423408,1.1739845031423408,1.1739845031423408, \
+	quaternions[i][0],quaternions[i][1], quaternions[i][2],quaternions[i][3]))
+ 
+    out.write('\n')
+    out.write('# Bond topology\n')
+    out.write('Bonds\n')
+    out.write('\n')
+
+    for i in range(nbonds):
+        if i < nbonds-2:
+             out.write("%d  %d  %d  %d\n" % (i+1,1,bonds[i][0],bonds[i][1]))
+        #else:
+        
+        #out.write("%d  %d  %d  %d\n" % (i+1,2,bonds[i][0],bonds[i][1]))
+
+    out.close()
+
+    print("## Wrote data to 'data.oxdna'", file=sys.stdout)
+    print("## DONE", file=sys.stdout)
+
+# call the above main() function, which executes the program
+read_strands (infile)
+
+end_time=timer()
+runtime = end_time-start_time
+hours = runtime/3600
+minutes = (runtime-np.rint(hours)*3600)/60
+seconds = (runtime-np.rint(hours)*3600-np.rint(minutes)*60)%60
+print("## Total runtime %ih:%im:%.2fs" % (hours,minutes,seconds), file=sys.stdout)

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

@@ -0,0 +1,87 @@
+variable number	equal 4
+variable ofreq	equal 1000
+variable efreq	equal 1000
+
+variable ntype equal 4
+
+variable T equal 300.0
+variable rhos   equal 0.2
+
+units real
+
+dimension 3
+
+newton on
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid oxdna
+atom_modify sort 0 8.518
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 17.036 bin 
+neigh_modify every 10 delay 0 check yes
+
+read_data data.duplex4.4type
+
+mass * 315.8376           # sets per-type mass if not in data file
+set atom * mass 315.8376  # sets per-atom mass
+
+group all type 1 4
+
+# oxDNA2 bond interactions - FENE backbone
+bond_style oxdna2/fene 
+bond_coeff * 11.92337812042065 2.1295 6.4430152
+special_bonds lj 0 1 1
+
+# oxDNA pair interactions
+pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh 
+pair_coeff * * oxdna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576
+pair_coeff * * oxdna2/stk seqdep ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
+
+label loop
+variable base loop ${ntype} 
+  variable basemod equal ${base}%4
+  if "${basemod} == 1" then &
+    "variable comp equal ${base}+3" &
+    "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45"
+  if "${basemod} == 2" then &
+    "variable comp equal ${base}+1" &
+    "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45"
+next base
+jump in.duplex4.4type loop
+
+pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 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 4.80673207785863 3.4072 5.1108 1.87396 4.94044 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
+
+# Langevin dynamics
+fix 1 all nve/asphere
+fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10
+
+timestep 0.01706
+
+#comm_style tiled
+fix 3 all balance 1000 1.03 shift xyz 10 1.03
+comm_modify cutoff 32.4
+
+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 1000000
+
+write_data last_config.${number}.* nocoeff
+#write_restart last_config.${number}.*

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

@@ -0,0 +1,87 @@
+variable number	equal 8
+variable ofreq	equal 1000
+variable efreq	equal 1000
+
+variable ntype equal 8
+
+variable T equal 300.0
+variable rhos   equal 0.2
+
+units real
+
+dimension 3
+
+newton on
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid oxdna
+atom_modify sort 0 8.518
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 17.036 bin 
+neigh_modify every 10 delay 0 check yes
+
+read_data data.duplex4.8type
+
+mass * 315.8376           # sets per-type mass if not in data file
+set atom * mass 315.8376  # sets per-atom mass
+
+group all type 1 4
+
+# oxDNA2 bond interactions - FENE backbone
+bond_style oxdna2/fene 
+bond_coeff * 11.92337812042065 2.1295 6.4430152
+special_bonds lj 0 1 1
+
+# oxDNA pair interactions
+pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh 
+pair_coeff * * oxdna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576
+pair_coeff * * oxdna2/stk seqdep ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
+
+label loop
+variable base loop ${ntype} 
+  variable basemod equal ${base}%4
+  if "${basemod} == 1" then &
+    "variable comp equal ${base}+3" &
+    "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45"
+  if "${basemod} == 2" then &
+    "variable comp equal ${base}+1" &
+    "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45"
+next base
+jump in.duplex4.8type loop
+
+pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 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 4.80673207785863 3.4072 5.1108 1.87396 4.94044 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
+
+# Langevin dynamics
+fix 1 all nve/asphere
+fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10
+
+timestep 0.01706
+
+#comm_style tiled
+fix 3 all balance 1000 1.03 shift xyz 10 1.03
+comm_modify cutoff 32.4
+
+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 1000000
+
+write_data last_config.${number}.* nocoeff
+#write_restart last_config.${number}.*

examples/PACKAGES/cgdna/examples/real_units/oxRNA2/duplex2/data.duplex2

@@ -0,0 +1,91 @@
+LAMMPS data file in real units via oxdna lj2real.py, date 2024-05-19
+
+16 atoms
+4 atom types
+13 bonds
+1 bond types
+16 ellipsoids
+
+-170 170 xlo xhi
+-170 170 ylo yhi
+-170 170 zlo zhi
+
+Masses
+
+1 315.8376
+2 315.8376
+3 315.8376
+4 315.8376
+
+Atoms # hybrid
+
+1 1 -5.224492277936935 -5.6003990662830665 3.072035980595378 1 1 1.0016462505133576 0 0 0
+2 2 -3.855482258589815 -8.54410812515585 6.182955020430966 1 1 1.0016462505133576 0 0 0
+3 3 -0.8418698080395857 -10.56041032511679 9.10967975032824 1 1 1.0016462505133576 0 0 0
+4 4 2.502394065492512 -10.715431837829685 12.145744722571814 1 1 1.0016462505133576 0 0 0
+5 1 5.355178690564601 -8.674171903962998 15.067785212133312 1 1 1.0016462505133576 0 0 0
+6 2 6.7305169669220595 -5.763569949980494 18.347908888941284 1 1 1.0016462505133576 0 0 0
+7 3 6.061219006086631 -3.4238594469157198 21.88758604427721 1 1 1.0016462505133576 0 0 0
+8 4 4.001186577913306 -2.576839632838177 26.12300846270287 1 1 1.0016462505133576 0 0 0
+9 1 3.454997351061381 -12.298079702286948 26.05718083554597 2 1 1.0016462505133576 0 0 0
+10 2 -0.2728181587270111 -11.028698363238112 23.169872406755868 2 1 1.0016462505133576 0 0 0
+11 3 -2.692868178466912 -7.73787195036868 20.549852065183913 2 1 1.0016462505133576 0 0 0
+12 4 -3.316857346830113 -4.145374554885233 17.08862230448963 2 1 1.0016462505133576 0 0 0
+13 1 -0.5308965342198838 -0.6095451431748122 13.28229291571604 3 1 1.0016462505133576 0 0 0
+14 2 1.5233668194980015 -0.46991432454420656 8.699204689407908 3 1 1.0016462505133576 0 0 0
+15 3 3.844548159551531 -2.026909836907328 5.074452450044903 3 1 1.0016462505133576 0 0 0
+16 4 4.325141724684425 -4.740799489595668 1.4104749932020408 3 1 1.0016462505133576 0 0 0
+
+Velocities
+
+1 0.00026896558742537556 0.00011298695236274073 0.001242364337461123 0.7538466533118467 -1.2587520584415195 -1.1163576881067447
+2 -0.00019946914535880285 0.0013465785184092233 -0.0009479872206420321 -0.13024003640483983 -0.5006975787807386 0.17048535791572514
+3 -0.0010377647810347322 -0.0006804774738725614 -0.000302697462953215 -0.15638545864527348 -0.2683843524758034 -0.6295604792026762
+4 -0.0011968051721949484 -0.002808404437492725 0.00016214368951061121 -0.7029471277015998 1.2169631204234201 1.42700472482703
+5 -0.0008046113463391788 -0.001142874812754601 -0.0006767129075723855 0.304218367349499 -0.4005571162913614 0.5710347488390389
+6 -0.00023475461149269044 0.000959484075931813 0.0007283860029089665 0.3921776444343422 -2.399417440979843 0.3950910265578085
+7 0.0002545632912247854 -0.00019202725318668095 -0.0007112078778547229 1.4800522749729792 1.8058703404340948 -0.5778414965351256
+8 0.0018887377488028885 -0.0002473511615838234 0.0008120520191337178 0.18841278062652408 0.3347372075847072 -0.5408605905745774
+9 0.0002452564077667799 0.00020601300929708606 6.1033299095680186e-05 0.13966147753401867 -0.0005390290197378453 0.6635632318913824
+10 0.000968244047328249 0.0005529827424647325 -0.00020224034557198784 -0.7235582069719148 -1.9412262416735993 -1.289806869224333
+11 -0.0017543321990246556 -0.000939796984860897 0.0018048542648271923 -1.5775475529872025 -2.0891633737315023 0.40142307521789933
+12 -0.0005934853675296159 0.001116191652783757 4.626275649966328e-05 -1.200961814632207 0.4371811217355096 0.43287366246768927
+13 -0.0007222905985558083 -0.0005767904238661645 0.0006648020330562531 -1.084763819731394 1.1718860080947717 0.2470159472481526
+14 0.0002573730178578412 -0.00182797610679242 -0.00033107273492769625 -0.510496177490122 0.29118940603730814 0.9195837620128926
+15 -0.0010092903785878923 0.0011654195253227475 4.0609661125969864e-05 -0.723803934131871 0.07956576746268508 -1.1413793944128399
+16 -0.0009587558806876301 -0.0004046946607553641 -0.0002343452641922075 0.07373406158203998 -1.3986322243084912 0.4617216556119086
+
+Bonds
+
+1 1 1 2
+2 1 2 3
+3 1 3 4
+4 1 4 5
+5 1 5 6
+6 1 6 7
+7 1 7 8
+8 1 9 10
+9 1 10 11
+10 1 11 12
+11 1 13 14
+12 1 14 15
+13 1 15 16
+
+Ellipsoids
+
+1 9.999999997766462 9.999999997766462 9.999999997766462 0.9964752158482045 -0.053253555733239796 0.011391163807102514 -0.06380787090289707
+2 9.999999997766462 9.999999997766462 9.999999997766462 0.9369923833143513 0.11220716044648564 0.06732538499716349 0.3239168400846305
+3 9.999999997766462 9.999999997766462 9.999999997766462 0.797964932091827 0.14473096354527873 0.18374142699366386 0.5554673737937029
+4 9.999999997766462 9.999999997766462 9.999999997766462 0.5660864821344559 0.14688275499481052 0.09873742533340191 0.8051226439917721
+5 9.999999997766462 9.999999997766462 9.999999997766462 0.2533023785125306 0.12062313161679827 0.08583012223905846 0.9559922359911086
+6 9.999999997766462 9.999999997766462 9.999999997766462 -0.03855807343534716 0.08405913137017908 0.02236505169306371 0.9954632800204194
+7 9.999999997766462 9.999999997766462 9.999999997766462 -0.45592844330248017 0.1004550065061007 -0.052524745294758785 0.8827679181910482
+8 9.999999997766462 9.999999997766462 9.999999997766462 0.768021221540491 -0.009582139884533599 0.03658677589040892 -0.63930665074644
+9 9.999999997766462 9.999999997766462 9.999999997766462 -0.23299975754512345 0.688686395231341 0.6747873944883376 -0.12682324016841584
+10 9.999999997766462 9.999999997766462 9.999999997766462 -0.24662061871907232 0.8744456399178389 0.39370836087823996 -0.13970261209395163
+11 9.999999997766462 9.999999997766462 9.999999997766462 -0.087475900850909 0.977367602388229 0.14493549113095577 -0.12686307572668784
+12 9.999999997766462 9.999999997766462 9.999999997766462 -0.03181169300779214 0.9634374984140112 -0.2442360692534371 -0.10547485630879185
+13 9.999999997766462 9.999999997766462 9.999999997766462 -0.032786070696572266 0.7922941528811777 -0.6084214170523915 -0.03191282109962717
+14 9.999999997766462 9.999999997766462 9.999999997766462 0.047188686288341455 0.6316396208287698 -0.7737349519945348 0.011783095844627799
+15 9.999999997766462 9.999999997766462 9.999999997766462 -0.05869980642620335 -0.34229358203414423 0.9376740835056508 0.012519965878508689
+16 9.999999997766462 9.999999997766462 9.999999997766462 -0.08582818143150042 0.0008707732197394232 0.9939540921464659 -0.0684691735853161

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

@@ -0,0 +1,74 @@
+# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19
+variable number	equal 2
+variable ofreq	equal 1000
+variable efreq	equal 1000
+variable T      equal 300.0
+variable rhos   equal 0.5
+
+units real
+
+dimension 3
+
+newton on
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid oxdna
+atom_modify sort 0 8.518
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 17.036 bin
+neigh_modify every 1 delay 0 check yes
+
+read_data data.duplex2
+
+set atom * mass 315.8376
+
+group all type 1 4
+
+# oxRNA2 bond interactions - FENE backbone
+bond_style oxrna2/fene
+bond_coeff * 11.92337812042065 2.1295 6.482800913
+special_bonds lj 0 1 1
+
+# oxRNA2 pair interactions
+pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh
+pair_coeff * * oxrna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576
+pair_coeff * * oxrna2/stk seqdep ${T} 8.35864576375849 0.005504556 0.70439070204273 3.66274 7.92174 2.9813 6.64404 0.9 0.0 0.95 0.9 0.0 0.95 1.3 0.0 0.8 1.3 0.0 0.8 2.0 0.65 2.0 0.65
+pair_coeff * * oxrna2/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxrna2/hbond seqdep 5.18928666388042 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxrna2/hbond seqdep 5.18928666388042 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 3 4 oxrna2/hbond seqdep 5.18928666388042 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxrna2/xstk 4.92690859644113 4.259 5.1108 3.57756 4.94044 2.25 0.505 0.58 1.7 1.266 0.68 1.7 1.266 0.68 1.7 0.309 0.68 1.7 0.309 0.68
+pair_coeff * * oxrna2/coaxstk 6.57330882442206 4.259 5.1108 3.57756 4.94044 2.0 2.592 0.65 1.3 0.151 0.8 0.9 0.685 0.95 0.9 0.685 0.95 2.0 -0.65 2.0 -0.65
+pair_coeff * * oxrna2/dh ${T} ${rhos} 1.02455
+
+# NVE ensemble
+fix 1 all nve/asphere
+#fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10
+
+timestep 0.01706
+
+#comm_style tiled
+fix 3 all balance 1000 1.03 shift xyz 10 1.03
+comm_modify cutoff 32.4
+
+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 1000000
+
+write_data last_config.${number}.* nocoeff
+#write_restart last_config.${number}.*

examples/PACKAGES/cgdna/examples/real_units/oxRNA2/potential_file/data.duplex2

@@ -0,0 +1,91 @@
+LAMMPS data file in real units via oxdna lj2real.py, date 2024-05-19
+
+16 atoms
+4 atom types
+13 bonds
+1 bond types
+16 ellipsoids
+
+-170 170 xlo xhi
+-170 170 ylo yhi
+-170 170 zlo zhi
+
+Masses
+
+1 315.8376
+2 315.8376
+3 315.8376
+4 315.8376
+
+Atoms # hybrid
+
+1 1 -5.224492277936935 -5.6003990662830665 3.072035980595378 1 1 1.0016462505133576 0 0 0
+2 2 -3.855482258589815 -8.54410812515585 6.182955020430966 1 1 1.0016462505133576 0 0 0
+3 3 -0.8418698080395857 -10.56041032511679 9.10967975032824 1 1 1.0016462505133576 0 0 0
+4 4 2.502394065492512 -10.715431837829685 12.145744722571814 1 1 1.0016462505133576 0 0 0
+5 1 5.355178690564601 -8.674171903962998 15.067785212133312 1 1 1.0016462505133576 0 0 0
+6 2 6.7305169669220595 -5.763569949980494 18.347908888941284 1 1 1.0016462505133576 0 0 0
+7 3 6.061219006086631 -3.4238594469157198 21.88758604427721 1 1 1.0016462505133576 0 0 0
+8 4 4.001186577913306 -2.576839632838177 26.12300846270287 1 1 1.0016462505133576 0 0 0
+9 1 3.454997351061381 -12.298079702286948 26.05718083554597 2 1 1.0016462505133576 0 0 0
+10 2 -0.2728181587270111 -11.028698363238112 23.169872406755868 2 1 1.0016462505133576 0 0 0
+11 3 -2.692868178466912 -7.73787195036868 20.549852065183913 2 1 1.0016462505133576 0 0 0
+12 4 -3.316857346830113 -4.145374554885233 17.08862230448963 2 1 1.0016462505133576 0 0 0
+13 1 -0.5308965342198838 -0.6095451431748122 13.28229291571604 3 1 1.0016462505133576 0 0 0
+14 2 1.5233668194980015 -0.46991432454420656 8.699204689407908 3 1 1.0016462505133576 0 0 0
+15 3 3.844548159551531 -2.026909836907328 5.074452450044903 3 1 1.0016462505133576 0 0 0
+16 4 4.325141724684425 -4.740799489595668 1.4104749932020408 3 1 1.0016462505133576 0 0 0
+
+Velocities
+
+1 0.00026896558742537556 0.00011298695236274073 0.001242364337461123 0.7538466533118467 -1.2587520584415195 -1.1163576881067447
+2 -0.00019946914535880285 0.0013465785184092233 -0.0009479872206420321 -0.13024003640483983 -0.5006975787807386 0.17048535791572514
+3 -0.0010377647810347322 -0.0006804774738725614 -0.000302697462953215 -0.15638545864527348 -0.2683843524758034 -0.6295604792026762
+4 -0.0011968051721949484 -0.002808404437492725 0.00016214368951061121 -0.7029471277015998 1.2169631204234201 1.42700472482703
+5 -0.0008046113463391788 -0.001142874812754601 -0.0006767129075723855 0.304218367349499 -0.4005571162913614 0.5710347488390389
+6 -0.00023475461149269044 0.000959484075931813 0.0007283860029089665 0.3921776444343422 -2.399417440979843 0.3950910265578085
+7 0.0002545632912247854 -0.00019202725318668095 -0.0007112078778547229 1.4800522749729792 1.8058703404340948 -0.5778414965351256
+8 0.0018887377488028885 -0.0002473511615838234 0.0008120520191337178 0.18841278062652408 0.3347372075847072 -0.5408605905745774
+9 0.0002452564077667799 0.00020601300929708606 6.1033299095680186e-05 0.13966147753401867 -0.0005390290197378453 0.6635632318913824
+10 0.000968244047328249 0.0005529827424647325 -0.00020224034557198784 -0.7235582069719148 -1.9412262416735993 -1.289806869224333
+11 -0.0017543321990246556 -0.000939796984860897 0.0018048542648271923 -1.5775475529872025 -2.0891633737315023 0.40142307521789933
+12 -0.0005934853675296159 0.001116191652783757 4.626275649966328e-05 -1.200961814632207 0.4371811217355096 0.43287366246768927
+13 -0.0007222905985558083 -0.0005767904238661645 0.0006648020330562531 -1.084763819731394 1.1718860080947717 0.2470159472481526
+14 0.0002573730178578412 -0.00182797610679242 -0.00033107273492769625 -0.510496177490122 0.29118940603730814 0.9195837620128926
+15 -0.0010092903785878923 0.0011654195253227475 4.0609661125969864e-05 -0.723803934131871 0.07956576746268508 -1.1413793944128399
+16 -0.0009587558806876301 -0.0004046946607553641 -0.0002343452641922075 0.07373406158203998 -1.3986322243084912 0.4617216556119086
+
+Bonds
+
+1 1 1 2
+2 1 2 3
+3 1 3 4
+4 1 4 5
+5 1 5 6
+6 1 6 7
+7 1 7 8
+8 1 9 10
+9 1 10 11
+10 1 11 12
+11 1 13 14
+12 1 14 15
+13 1 15 16
+
+Ellipsoids
+
+1 9.999999997766462 9.999999997766462 9.999999997766462 0.9964752158482045 -0.053253555733239796 0.011391163807102514 -0.06380787090289707
+2 9.999999997766462 9.999999997766462 9.999999997766462 0.9369923833143513 0.11220716044648564 0.06732538499716349 0.3239168400846305
+3 9.999999997766462 9.999999997766462 9.999999997766462 0.797964932091827 0.14473096354527873 0.18374142699366386 0.5554673737937029
+4 9.999999997766462 9.999999997766462 9.999999997766462 0.5660864821344559 0.14688275499481052 0.09873742533340191 0.8051226439917721
+5 9.999999997766462 9.999999997766462 9.999999997766462 0.2533023785125306 0.12062313161679827 0.08583012223905846 0.9559922359911086
+6 9.999999997766462 9.999999997766462 9.999999997766462 -0.03855807343534716 0.08405913137017908 0.02236505169306371 0.9954632800204194
+7 9.999999997766462 9.999999997766462 9.999999997766462 -0.45592844330248017 0.1004550065061007 -0.052524745294758785 0.8827679181910482
+8 9.999999997766462 9.999999997766462 9.999999997766462 0.768021221540491 -0.009582139884533599 0.03658677589040892 -0.63930665074644
+9 9.999999997766462 9.999999997766462 9.999999997766462 -0.23299975754512345 0.688686395231341 0.6747873944883376 -0.12682324016841584
+10 9.999999997766462 9.999999997766462 9.999999997766462 -0.24662061871907232 0.8744456399178389 0.39370836087823996 -0.13970261209395163
+11 9.999999997766462 9.999999997766462 9.999999997766462 -0.087475900850909 0.977367602388229 0.14493549113095577 -0.12686307572668784
+12 9.999999997766462 9.999999997766462 9.999999997766462 -0.03181169300779214 0.9634374984140112 -0.2442360692534371 -0.10547485630879185
+13 9.999999997766462 9.999999997766462 9.999999997766462 -0.032786070696572266 0.7922941528811777 -0.6084214170523915 -0.03191282109962717
+14 9.999999997766462 9.999999997766462 9.999999997766462 0.047188686288341455 0.6316396208287698 -0.7737349519945348 0.011783095844627799
+15 9.999999997766462 9.999999997766462 9.999999997766462 -0.05869980642620335 -0.34229358203414423 0.9376740835056508 0.012519965878508689
+16 9.999999997766462 9.999999997766462 9.999999997766462 -0.08582818143150042 0.0008707732197394232 0.9939540921464659 -0.0684691735853161