Unverified Commit 2ad93551 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer Committed by GitHub
Browse files

Merge pull request #1383 from akohlmey/final-changes-for-patch

Several small changes and tweaks for patch release
parents e63d2cee b685a0a7
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+3 −3
Original line number Diff line number Diff line
@@ -5,15 +5,15 @@ set(temp_git_describe "(unknown)")
set(temp_git_info "false")
if(GIT_FOUND AND EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/../.git)
  set(temp_git_info "true")
  execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/../.git rev-parse HEAD
  execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/.. rev-parse HEAD
    OUTPUT_VARIABLE temp_git_commit
    ERROR_QUIET
    OUTPUT_STRIP_TRAILING_WHITESPACE)
  execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/../.git rev-parse --abbrev-ref HEAD
  execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/.. rev-parse --abbrev-ref HEAD
    OUTPUT_VARIABLE temp_git_branch
    ERROR_QUIET
    OUTPUT_STRIP_TRAILING_WHITESPACE)
  execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/../.git describe --dirty=-modified
  execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/.. describe --dirty=-modified
    OUTPUT_VARIABLE temp_git_describe
    ERROR_QUIET
    OUTPUT_STRIP_TRAILING_WHITESPACE)
+8 −8
Original line number Diff line number Diff line
@@ -116,6 +116,13 @@ mobi: epub
	@echo "Conversion finished. The MOBI manual file is created."

pdf: $(OBJECTS) $(ANCHORCHECK)
	@(\
		cd src/Developer; \
		pdflatex developer; \
		pdflatex developer; \
		mv developer.pdf ../../Developer.pdf; \
		cd ../../; \
	)
	@(\
                . $(VENV)/bin/activate ;\
                cp -r src/* $(RSTDIR)/ ;\
@@ -136,13 +143,6 @@ pdf: $(OBJECTS) $(ANCHORCHECK)
	  make && \
	  mv LAMMPS.pdf ../Manual.pdf && \
	  cd ../;
	@(\
		cd src/Developer; \
		pdflatex developer; \
		pdflatex developer; \
		mv developer.pdf ../../Developer.pdf; \
		cd ../../; \
	)
	@rm -rf latex/_sources
	@rm -rf latex/PDF
	@rm -rf latex/USER
+6 −6
Original line number Diff line number Diff line
@@ -49,7 +49,7 @@
     22      0      1  25.100   0.000   0.000
     23      0      1  26.295   0.000   0.000
     24    110      2  27.490   0.000   0.000
     25    128      2  28.685   0.000   0.000
     25    128      2  28.685  35.85686 0.000
     26      0      1  29.881   0.000   0.000
     27      0      1  31.076   0.000   0.000
     28      0      1  32.271   0.000   0.000
@@ -175,7 +175,7 @@
    148      0      1  32.271   4.781   0.000
    149      0      1  33.466   4.781   0.000
    150      0      1  34.662   4.781   0.000
    151     53      2   0.000   5.976   0.000
    151     53      2 35.85686  5.976   0.000
    152      0      1   1.195   5.976   0.000
    153      0      1   2.390   5.976   0.000
    154      0      1   3.586   5.976   0.000
@@ -655,7 +655,7 @@
    628      0      1  32.271  23.905   0.000
    629      0      1  33.466  23.905   0.000
    630      0      1  34.662  23.905   0.000
    631    148      2   0.000  25.100   0.000
    631    148      2 35.85686 25.100   0.000
    632      0      1   1.195  25.100   0.000
    633      0      1   2.390  25.100   0.000
    634      0      1   3.586  25.100   0.000
@@ -976,7 +976,7 @@
    949     25      3   0.677  33.143   0.000
    950     25      4   1.353  32.819   0.000
    951     26      3  35.071  18.557   0.000
    952     26      4  35.480  19.186   0.000
    952     26      4 35.48000 19.186   0.000
    953     27      3  29.131  15.504   0.000
    954     27      4  28.382  15.470   0.000
    955     28      3  23.456  33.395   0.000
@@ -1096,7 +1096,7 @@
   1069     85      3  33.021  33.461   0.000
   1070     85      4  33.771  33.455   0.000
   1071     86      3   0.552  18.315   0.000
   1072     86      4  35.766  18.701   0.000
   1072     86      4 -0.09086 18.701   0.000
   1073     87      3  28.026  32.796   0.000
   1074     87      4  28.562  33.321   0.000
   1075     88      3  24.351  29.925   0.000
@@ -1112,7 +1112,7 @@
   1085     93      3  26.170  16.278   0.000
   1086     93      4  26.046  17.017   0.000
   1087     94      3  10.380   0.547   0.000
   1088     94      4  10.003  35.755   0.000
   1088     94      4  10.003 -0.10186  0.000
   1089     95      3   0.419  29.308   0.000
   1090     95      4   0.837  29.930   0.000
   1091     96      3  13.712  28.191   0.000
+86 −0
Original line number Diff line number Diff line
# 2d micelle simulation

dimension	2

neighbor	0.3 bin
neigh_modify	delay 5

atom_style	bond

# Soft potential push-off

read_data	data.micelle
special_bonds	fene

pair_style	soft 1.12246
pair_coeff	* * 0.0 1.12246

bond_style 	harmonic
bond_coeff	1 50.0 0.75

velocity	all create 0.45 2349852

variable	prefactor equal ramp(1.0,20.0)

fix		1 all nve
fix		2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix		3 all adapt 1 pair soft a * * v_prefactor
fix		4 all enforce2d

thermo		50
run		1000

unfix		3

# Main run

pair_style	lj/cut 2.5

# solvent/head - full-size and long-range

pair_coeff	1 1 1.0 1.0 2.5
pair_coeff	2 2 1.0 1.0 2.5
pair_coeff	1 2 1.0 1.0 2.5

# tail/tail - size-averaged and long-range

pair_coeff	3 3 1.0 0.75 2.5
pair_coeff	4 4 1.0 0.50 2.5
pair_coeff	3 4 1.0 0.67 2.5

# solvent/tail - full-size and repulsive

pair_coeff	1 3 1.0 1.0 1.12246
pair_coeff	1 4 1.0 1.0 1.12246

# head/tail - size-averaged and repulsive

pair_coeff	2 3 1.0 0.88 1.12246
pair_coeff	2 4 1.0 0.75 1.12246

thermo		1000

#dump		1 all atom 2000 dump.micelle

#dump		2 all image 2000 image.*.jpg type type zoom 1.6
#dump_modify	2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75

#dump		3 all movie 2000 movie.mpg type type zoom 1.6
#dump_modify	3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75

reset_timestep	0
group solvent   molecule 0
group solute    subtract all solvent
unfix 1
unfix 2
unfix 4
fix		1 solvent nve
fix		2 solvent temp/rescale 100 0.45 0.45 0.02 1.0
fix		5 solute rigid molecule langevin 0.45 0.45 0.5 112211
fix		4 all enforce2d
run		20000
unfix 5
unfix 4
fix		5 solute rigid/small molecule langevin 0.45 0.45 0.5 112211
fix		4 all enforce2d
run		20000
+259 −0
Original line number Diff line number Diff line
LAMMPS (27 Nov 2018)
LAMMPS (28 Feb 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
  using 1 OpenMP thread(s) per MPI task
# 2d micelle simulation

@@ -24,9 +25,12 @@ read_data data.micelle
  1 = max # of 1-3 neighbors
  1 = max # of 1-4 neighbors
  2 = max # of special neighbors
  special bonds CPU = 0.000394821 secs
  read_data CPU = 0.00212336 secs
special_bonds	fene
  2 = max # of 1-2 neighbors
  2 = max # of special neighbors
  special bonds CPU = 0.00018549 secs

pair_style	soft 1.12246
pair_coeff	* * 0.0 1.12246
@@ -80,21 +84,21 @@ Step Temp E_pair E_mol TotEng Press
     900         0.45   0.47785593   0.10150857    1.0289895    5.7765975 
     950   0.49590559   0.46050477  0.096404887     1.052402    5.8649245 
    1000         0.45   0.47691182   0.08808163    1.0146185    6.0177568 
Loop time of 0.167265 on 1 procs for 1000 steps with 1200 atoms
Loop time of 0.113919 on 1 procs for 1000 steps with 1200 atoms

Performance: 2582728.958 tau/day, 5978.539 timesteps/s
99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 3792167.464 tau/day, 8778.165 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.096171   | 0.096171   | 0.096171   |   0.0 | 57.50
Bond    | 0.006212   | 0.006212   | 0.006212   |   0.0 |  3.71
Neigh   | 0.024826   | 0.024826   | 0.024826   |   0.0 | 14.84
Comm    | 0.0047672  | 0.0047672  | 0.0047672  |   0.0 |  2.85
Output  | 0.00029063 | 0.00029063 | 0.00029063 |   0.0 |  0.17
Modify  | 0.028771   | 0.028771   | 0.028771   |   0.0 | 17.20
Other   |            | 0.006227   |            |       |  3.72
Pair    | 0.076825   | 0.076825   | 0.076825   |   0.0 | 67.44
Bond    | 0.0041864  | 0.0041864  | 0.0041864  |   0.0 |  3.67
Neigh   | 0.017061   | 0.017061   | 0.017061   |   0.0 | 14.98
Comm    | 0.0019042  | 0.0019042  | 0.0019042  |   0.0 |  1.67
Output  | 0.00017285 | 0.00017285 | 0.00017285 |   0.0 |  0.15
Modify  | 0.011218   | 0.011218   | 0.011218   |   0.0 |  9.85
Other   |            | 0.002551   |            |       |  2.24

Nlocal:    1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -164,92 +168,92 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 4.024 | 4.024 | 4.024 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0         0.45   -1.7056163   0.08808163   -1.1679097    3.9431686 
    1000         0.45   -1.9727655  0.058608715   -1.4645318    1.9982298 
    2000   0.46465361   -1.9897467  0.067008449   -1.4584719    1.5873463 
    3000   0.46175071   -2.0129279  0.057865385   -1.4936966      1.41269 
    4000   0.44386154   -2.0280304  0.067167835   -1.5173709    1.4022093 
    5000   0.46127582   -2.0556041  0.068318674    -1.526394    1.1416711 
    6000   0.45354052   -2.0463246   0.05461954   -1.5385425    1.1650258 
    7000   0.44082313    -2.040263  0.060218047   -1.5395891    1.3258681 
    8000   0.44353466   -2.0423792  0.061769402   -1.5374447    1.2696989 
    9000   0.46192977   -2.0761348  0.064999109   -1.5495908    0.9205826 
   10000   0.45278646   -2.0589872  0.059623919   -1.5469542     1.075581 
   11000   0.45583355   -2.0661957  0.058197558   -1.5525445     1.127643 
   12000   0.45881198   -2.0921508  0.066937896   -1.5667833   0.98383574 
   13000   0.45339481    -2.079088   0.06292782   -1.5631432    1.0188637 
   14000   0.43601312   -2.0624084  0.057999616    -1.568759    1.1452177 
   15000   0.45941503   -2.0746606  0.062523373    -1.553105   0.86928343 
   16000         0.45   -2.0743162   0.05517924    -1.569512   0.86849848 
   17000   0.45603004   -2.0657683  0.058711872   -1.5514064   0.95544551 
   18000   0.45320383   -2.1009711  0.060716634   -1.5874283    0.8343521 
   19000   0.44072983   -2.0846408  0.062893297    -1.581385   0.90776246 
   20000   0.44452441   -2.0921415  0.060341571    -1.587646   0.98180005 
   21000   0.45964557   -2.0837047  0.054459432   -1.5699827    1.0213779 
   22000   0.46351849   -2.1053613  0.058392027   -1.5838371   0.81579487 
   23000   0.45576065   -2.1001888  0.057646538   -1.5871614   0.76090085 
   24000   0.44671746   -2.0848717  0.058192801   -1.5803337   0.77003809 
   25000   0.44371239   -2.0870872  0.054804981   -1.5889396   0.92295746 
   26000   0.45381188    -2.097021  0.057195346    -1.586392    0.7743058 
   27000   0.46158533   -2.1071056  0.061289644   -1.5846153   0.78981802 
   28000   0.46534671   -2.1056151  0.054934755   -1.5857214   0.80778664 
   29000    0.4505804   -2.0949318  0.065503451   -1.5792234   0.78274755 
   30000   0.45730883   -2.1029161  0.063461968   -1.5825264   0.82507857 
   31000    0.4620071   -2.1124989  0.059980378   -1.5908964   0.78583986 
   32000   0.46934619   -2.1107818  0.056442616   -1.5853842   0.70535653 
   33000   0.45800203   -2.1062502  0.054317859    -1.594312     0.726293 
   34000   0.44634295    -2.110401  0.057764968    -1.606665   0.85401059 
   35000    0.4431929   -2.1274759  0.062048133   -1.6226042   0.64243758 
   36000   0.46049645   -2.1300979  0.068463634   -1.6015216   0.57252544 
   37000   0.45366344   -2.0977407  0.053788554   -1.5906668   0.78046879 
   38000   0.44155077   -2.1166674  0.056888683   -1.6185959   0.53429042 
   39000   0.45631012    -2.096949   0.04860872   -1.5924104   0.86494908 
   40000   0.44684402   -2.1229137  0.067190397   -1.6092516   0.65110818 
   41000    0.4479377   -2.1105264  0.059375259   -1.6035867   0.79092862 
   42000   0.46143191   -2.1174539  0.057418393   -1.5989882   0.69762908 
   43000    0.4356786    -2.085826  0.056534028   -1.5939764   0.89541946 
   44000   0.45806826    -2.126423  0.060905733   -1.6078307   0.66389027 
   45000   0.44343688   -2.1116384  0.065870114    -1.602701   0.83947585 
   46000   0.43844672   -2.1096265  0.064158652   -1.6073865   0.77278902 
   47000   0.45794928   -2.1142786  0.058919562   -1.5977914   0.62611933 
   48000   0.45412335   -2.1106058  0.059153304   -1.5977076   0.66190677 
   49000   0.45927883   -2.1197656  0.068354598   -1.5925149   0.56008845 
   50000   0.44117285   -2.1020783  0.064763249   -1.5965099   0.85935147 
   51000   0.45325398   -2.1125154  0.062295387   -1.5973438   0.80951782 
   52000   0.43896579   -2.1039004  0.057475908   -1.6078245   0.84753768 
   53000   0.45180671   -2.1092446  0.063528598   -1.5942857   0.67065038 
   54000    0.4554341   -2.1185135  0.059603337   -1.6038556   0.76399618 
   55000   0.43861159   -2.0986406  0.057733879   -1.6026606   0.77334084 
   56000   0.45522991   -2.1207166  0.063287543   -1.6025785   0.78669598 
   57000   0.46125513   -2.1150202   0.06026261   -1.5938868   0.78148646 
   58000   0.45236938   -2.1088894  0.062678374   -1.5942186   0.75643518 
   59000   0.43927269   -2.1274165  0.055355076   -1.6331548   0.63495311 
   60000   0.45331102   -2.1336193  0.051244399   -1.6294416   0.56706921 
Loop time of 13.9361 on 1 procs for 60000 steps with 1200 atoms

Performance: 1859917.639 tau/day, 4305.365 timesteps/s
    1000         0.45   -1.9727644   0.05860769   -1.4645317    1.9982326 
    2000   0.46143408   -1.9889684  0.058103225   -1.4698156    1.7806269 
    3000   0.44459291   -1.9997961  0.068724164   -1.4868496    1.4369618 
    4000   0.46939549   -2.0330437  0.073499424   -1.4905399    1.3780016 
    5000   0.44411088   -2.0339936   0.05862049   -1.5316323    1.2544164 
    6000   0.44034597   -2.0265475  0.066481992   -1.5200864    1.2362891 
    7000   0.45097378   -2.0331083  0.058467565   -1.5240428    1.2762333 
    8000   0.45797632   -2.0330255  0.060048036   -1.5153828    1.3862396 
    9000   0.45297811   -2.0383417  0.067056519   -1.5186845    1.2762554 
   10000         0.45   -2.0628269  0.065650067   -1.5475518    1.0566213 
   11000   0.44466757   -2.0593977   0.06190999   -1.5531907    1.1452469 
   12000   0.46743534   -2.0684295  0.061056278   -1.5403274    1.0824225 
   13000   0.45601091   -2.0689708  0.054868536   -1.5584713   0.96703283 
   14000   0.44111882   -2.0553174  0.058249816   -1.5563164    1.0986427 
   15000   0.43894405   -2.0866829  0.064117804   -1.5839869   0.90031836 
   16000   0.43856814   -2.0879319  0.056024166    -1.593705   0.96387323 
   17000   0.45977841    -2.103188  0.058097306   -1.5856955   0.83352919 
   18000   0.43423341   -2.0813151  0.066623991   -1.5808196   0.98157638 
   19000   0.44245939   -2.0851261  0.057637655   -1.5853978   0.84228341 
   20000   0.43144678   -2.0895403   0.06536727   -1.5930858   0.88177768 
   21000   0.45014968    -2.106686  0.059137572   -1.5977739   0.89408935 
   22000    0.4575126   -2.1024115  0.063013023   -1.5822672   0.84886734 
   23000         0.45     -2.10897   0.06724784   -1.5920971   0.66205013 
   24000   0.43055602   -2.0894725  0.061566464   -1.5977089   0.81764789 
   25000    0.4366384   -2.0926743  0.059609321   -1.5967905   0.85549875 
   26000    0.4521714   -2.0963996  0.062031863   -1.5825731   0.80137118 
   27000   0.45734834   -2.1060987  0.061712636   -1.5874188   0.82899415 
   28000   0.44803467   -2.0859226  0.061871856   -1.5763894   0.97007526 
   29000         0.45   -2.1106243  0.063825481   -1.5971738   0.63798376 
   30000   0.44932806   -2.1006036  0.053053934    -1.598596   0.63907113 
   31000   0.44713779   -2.1096164  0.066470416   -1.5963808   0.66832708 
   32000    0.4373357   -2.0941237  0.058871613   -1.5982808   0.78176106 
   33000   0.44030485    -2.105644  0.058804306   -1.6069017   0.66286458 
   34000   0.43781175   -2.1233209  0.064611206   -1.6212628   0.56342584 
   35000   0.45670132   -2.1059408  0.053049584   -1.5965705   0.73992396 
   36000   0.45555427   -2.1149877  0.057627709   -1.6021854   0.85854939 
   37000   0.44134236   -2.1106202  0.064444306   -1.6052013   0.74674603 
   38000   0.44812623   -2.1003681  0.057266258   -1.5953491   0.78239359 
   39000   0.44167062     -2.11141     0.055354   -1.6147534    0.7066385 
   40000   0.46103176   -2.1166687  0.062155412   -1.5938657   0.73620955 
   41000   0.44537102   -2.0993898   0.05631213   -1.5980778   0.87348756 
   42000   0.44752506   -2.1115212  0.057506521   -1.6068625   0.72999561 
   43000    0.4483886   -2.1184719  0.066943915   -1.6035131   0.78112063 
   44000   0.45944897   -2.0916657  0.055242781   -1.5773568   0.98660473 
   45000   0.46238513   -2.1163075    0.0530031   -1.6013046   0.74416054 
   46000   0.45979064   -2.1165545  0.060657581   -1.5964895   0.63516974 
   47000   0.45936546   -2.1140678  0.049931919   -1.6051532   0.76425182 
   48000   0.45424613   -2.1122681  0.061885599   -1.5965149   0.71981142 
   49000   0.44449524   -2.1147361   0.06626748   -1.6043438   0.78720467 
   50000    0.4641185   -2.1114668  0.055104874   -1.5926302   0.70195865 
   51000   0.44220655   -2.1075773    0.0589109   -1.6068283   0.73806859 
   52000   0.43097906   -2.1189493  0.061502241   -1.6268271   0.69622593 
   53000         0.45    -2.137688  0.053631829   -1.6344311   0.48269158 
   54000   0.43777118   -2.1089246  0.047098534   -1.6244197   0.70423814 
   55000   0.46061985   -2.1129502  0.062520353   -1.5901938   0.72492307 
   56000    0.4524841   -2.1195648   0.06580089   -1.6016569   0.52709892 
   57000   0.44914574   -2.1041993  0.061040876    -1.594387    0.7979988 
   58000   0.46446286   -2.1181238  0.055741995    -1.598306   0.51009146 
   59000    0.4632674   -2.1169321  0.050672678   -1.6033781   0.83110911 
   60000   0.46340478    -2.122846  0.058485209   -1.6013422   0.69966471 
Loop time of 8.01683 on 1 procs for 60000 steps with 1200 atoms

Performance: 3233199.903 tau/day, 7484.259 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 9.2211     | 9.2211     | 9.2211     |   0.0 | 66.17
Bond    | 0.33763    | 0.33763    | 0.33763    |   0.0 |  2.42
Neigh   | 2.3772     | 2.3772     | 2.3772     |   0.0 | 17.06
Comm    | 0.37693    | 0.37693    | 0.37693    |   0.0 |  2.70
Output  | 0.0011795  | 0.0011795  | 0.0011795  |   0.0 |  0.01
Modify  | 1.2727     | 1.2727     | 1.2727     |   0.0 |  9.13
Other   |            | 0.3493     |            |       |  2.51
Pair    | 5.4027     | 5.4027     | 5.4027     |   0.0 | 67.39
Bond    | 0.23585    | 0.23585    | 0.23585    |   0.0 |  2.94
Neigh   | 1.5188     | 1.5188     | 1.5188     |   0.0 | 18.95
Comm    | 0.14452    | 0.14452    | 0.14452    |   0.0 |  1.80
Output  | 0.00060487 | 0.00060487 | 0.00060487 |   0.0 |  0.01
Modify  | 0.56352    | 0.56352    | 0.56352    |   0.0 |  7.03
Other   |            | 0.1508     |            |       |  1.88

Nlocal:    1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    405 ave 405 max 405 min
Nghost:    395 ave 395 max 395 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    9565 ave 9565 max 9565 min
Neighs:    9652 ave 9652 max 9652 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 9565
Ave neighs/atom = 7.97083
Total # of neighbors = 9652
Ave neighs/atom = 8.04333
Ave special neighs/atom = 0.5
Neighbor list builds = 4876
Neighbor list builds = 4886
Dangerous builds = 0
Total wall time: 0:00:14
Total wall time: 0:00:08
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