The tool lmp2arc.exe change my atom coordinate!!

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1

Hi all,
I have met a unusual issue when I use the lmp2arc.exe to convert my dump to arc file. From my dump file, the atom coordinate seems right, but when I use the command ./lmp2arc.exe -car my.car << EOF >> my.arc to complete my conversion. The precess finish narmally when ‘Program Exiting Normally’ comes. But when I check and edit my .arc file, I found the atomic coordinate became abnormal. The part of my dump and arc are attached. Someone know how to solve it? Many thanks!

DUMP

ITEM: TIMESTEP
2900000
ITEM: NUMBER OF ATOMS
2920
ITEM: BOX BOUNDS pp pp pp
2.5031787214614283e+01 4.9255812785385423e+01
1.4916536980138151e+01 5.9371063019865616e+01
2.2086443137469878e+01 5.2201156862525046e+01
ITEM: ATOMS id type x y z
720 1 30.2054 18.6944 27.0762
2013 6 34.0265 17.4714 25.7126
2018 6 34.3919 17.8999 23.6389
803 5 32.6887 20.0554 26.7086
805 6 32.5511 19.1564 27.2949
699 3 30.4836 19.361 25.873
704 3 31.7085 19.9203 25.5618
804 6 33.6857 20.0709 26.2271
700 3 29.474 19.2681 24.9226
709 6 28.5511 18.6151 25.1029
653 3 27.2139 20.518 26.996

…

********************!BIOSYM archive 3
PBC=ON
Frame 0 Number of Picoseconds = 1450.0000
!DATE Wed Mar 20 22:12:45 2019
PBC 24.2240 44.4545 30.1147 90.0000 90.0000 90.0000 (P1)
O1 1121.538451957 1217.756128279 1209.253306027 XXXX 1 oc O -0.1600
C2 974.941902069 990.793578142 964.661666403 XXXX 1 c5 C 0.0000
C3 954.724565664 1029.015594690 940.319885309 XXXX 1 cp C 0.0000
C4 942.837841935 906.441155681 943.951712156 XXXX 1 cp C 0.0000
C5 968.314263969 930.819972043 964.965749835 XXXX 1 c5 C 0.0000
C6 971.884882973 909.406271754 1003.530697448 XXXX 1 c5 C -0.0500
C7 927.007450835 853.015648494 956.892030284 XXXX 1 cp C 0.0000
C8 889.656410431 858.705839358 902.703604482 XXXX 1 cp C -0.1270
C9 900.276229746 919.181827864 894.780433226 XXXX 1 cp C 0.0000
C10 907.868045866 1040.329246469 897.029984329 XXXX 1 cp C 0.0000
C11 929.735037821 1001.973939602 917.565208353 XXXX 1 cp C 0.0000
C12 926.019062096 941.071201620 917.809152882 XXXX 1 cp C 0.0000
N13 980.741200915 956.510239656 1028.203615865 XXXX 1 npc N 0.0390
C14 981.853045839 953.656283640 1073.451046759 XXXX 1 c2 C 0.0880
H15 957.241463951 963.858589226 1087.891046476 XXXX 1 hc H 0.0530
C16 979.740706817 1070.749455033 1015.037504013 XXXX 1 c5 C 0.0000
C17 957.539385164 1091.305247273 946.493399325 XXXX 1 cp C 0.0000
C18 965.879700608 1109.980645487 986.395417986 XXXX 1 c5 C 0.0000

2

please note, that the lmp2arc tool has been unchanged since before LAMMPS was converted from fortran to c++, so it is unaware of many changes that have happened to LAMMPS and file formats since the last 15+ years.

that said, from looking at the test example provided with the lmp2arc tool it appears that it expects the trajectory file have scaled position data (xs, yz, zs) instead of the unscaled positions. hence all positions are multiplied by the corresponding box length.

axel.