NPT simulations
tomfrigato
tomfr... at hotmail.com
Wed Oct 8 10:18:23 UTC 2008
Hi all,
I did a simulation on 128 H2O box applying both thermostat and
barostat, so NPT ensamble.
I am not using the latest cp2k (21 july 2008 version).
I have 2 questions: the first one is about the barostat. Although I
went through the discussion there was already in this group (under
"barostat"), and read the reference paper (Martyna et al, JCP 101,
4177 (1994)), and used the suggested setup I found in the test file
cp2k/tests/Fist/H2O-32_NPT.inp
I see in my restart file run-1.restart at the end of the run that I
have 2 thermostat, one in the BAROSTAT section and one in the
THERMOSTAT section, with different coors, masses and velocities, and
honestly I still do not understand why one has 2 thermostats. My input
file is at the end of this post.
The second question is about some strange energy behaviour during the
run. I took the simulations coordinates and velocities from a previous
NVT simulations, and it looks like the setup I chose (BLYP, DZVP
basis) results in a more dense liquid. As the box shrinks there are
some large jumps in the total energy: for example this is a part of
the run-1.ener file:
33 16.500 0.577002245
317.150009889 -2199.101322770 -2198.365847076
82.407300000
34 17.000 0.579470429
318.506650669 -2199.103374256 -2198.365814097
93.484800000
35 17.500 0.584554875
321.301322756 -2199.107827624 -2198.365870421
94.342100000
36 18.000 0.591370574
325.047580217 -2198.642282517 -2197.894050509
101.114600000
37 18.500 0.598376710
328.898511501 -2198.649038164 -2197.894118726
122.682700000
38 19.000 0.604204462
332.101743054 -2198.654572558 -2197.894131860
111.490300000
as you see from step 35 to 36 the energy makes a huge jump.
I cannot attach the whole output files, but there are other jumps in
energies, and they always happen at given values of the cell size: if,
due to fluctuations, the cell size crosses again the value at which I
had seen an energy jump, the energy goes back to its previous value:
again from the energy file (see steps 1123-1124 and 1133-1134)
1221 610.500 0.591046245
324.869312116 -2198.746759475 -2197.893072489
89.885600000
1222 611.000 0.592657632
325.755013337 -2198.748370081 -2197.893090644
90.672400000
1223 611.500 0.593445612
326.188127577 -2198.749147687 -2197.893104641
90.380400000
1224 612.000 0.593277920
326.095955187 -2198.455662880 -2197.599816140
105.944200000
1225 612.500 0.592358652
325.590678712 -2198.454680205 -2197.599788503
116.352000000
1226 613.000 0.591168828
324.936690356 -2198.453420020 -2197.599765859
116.141900000
1227 613.500 0.590088019
324.342622042 -2198.452292381 -2197.599771406
95.207900000
1228 614.000 0.589119184
323.810100872 -2198.451302027 -2197.599795642
95.125000000
1229 614.500 0.588046292
323.220384100 -2198.450211148 -2197.599804872
95.287500000
1230 615.000 0.586837735
322.556099316 -2198.448987597 -2197.599789891
94.607400000
1231 615.500 0.585740577
321.953045182 -2198.447906730 -2197.599776478
84.758700000
1232 616.000 0.584965082
321.526793185 -2198.447193178 -2197.599783531
84.078000000
1233 616.500 0.584434830
321.235339807 -2198.446749014 -2197.599799740
84.934900000
1234 617.000 0.583845770
320.911562132 -2198.739006343 -2197.892564477
113.249800000
1235 617.500 0.582981114
320.436302633 -2198.738224089 -2197.892561054
124.694600000
1236 618.000 0.581865190
319.822934015 -2198.737172705 -2197.892552522
124.378000000
1237 618.500 0.580530383
319.089255611 -2198.735891778 -2197.892549785
101.654300000
Finally, my input file:
&GLOBAL
PREFERRED_FFT_LIBRARY FFTSG
PROJECT run
RUN_TYPE MD # # MD ## GEO_OPT ## ENERGY ----------
PRINT_LEVEL LOW
&END GLOBAL
&FORCE_EVAL
STRESS_TENSOR ANALYTICAL
&DFT
#UKS
#CHARGE -1
BASIS_SET_FILE_NAME /home/cocktail/frigato/tools/data/cp2k/
GTH_BASIS_SETS
POTENTIAL_FILE_NAME /home/cocktail/frigato/tools/data/cp2k/
POTENTIAL
&MGRID
CUTOFF 280
&END MGRID
&QS
EPS_DEFAULT 1.0E-12
EXTRAPOLATION PS
EXTRAPOLATION_ORDER 3
&END QS
&SCF
SCF_GUESS ATOMIC
MIXING 0.1
MAX_SCF 200
EPS_SCF 1.0E-6
&OT
MINIMIZER DIIS
&END OT
&END SCF
&XC
&XC_FUNCTIONAL BLYP
&END XC_FUNCTIONAL
&XC_GRID
XC_DERIV SPLINE2_SMOOTH
XC_SMOOTH_RHO NN10
&END XC_GRID
&END XC
&END DFT
&SUBSYS
&CELL
PERIODIC XYZ
ABC 15.6404 15.6404 15.6404
UNIT ANGSTROM
&END CELL
&COORD
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0.0015022320 -0.0015189177 0.0013237171
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0.0001264362 0.0006576714 0.0006746404
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0.0006409001 -0.0006011622 0.0003906506
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0.0001259314 -0.0003895500 -0.0004104882
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0.0003228084 0.0009620817 -0.0004719720
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0.0001708084 -0.0000560094 -0.0004404411
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0.0001700354 0.0000271232 -0.0003264908
0.0009981798 -0.0006805213 -0.0000543618
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0.0005160238 -0.0012890128 0.0004594615
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-0.0000623549 -0.0003280212 -0.0004445666
0.0000992097 -0.0007234760 -0.0001509300
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-0.0003152505 -0.0005391436 0.0007795889
-0.0006854506 -0.0006479979 -0.0007237669
-0.0006859213 -0.0003853558 0.0000630423
0.0003653908 0.0008834807 0.0001663788
-0.0001256093 0.0007753490 0.0000404585
-0.0000643365 -0.0000429437 0.0005392108
-0.0000085557 0.0006851354 -0.0001253411
0.0008988832 -0.0002842097 0.0021022182
-0.0006597173 0.0001419525 -0.0004343161
0.0004890521 -0.0006018432 0.0004103716
0.0017917043 0.0008180218 0.0010683800
-0.0001840742 -0.0014064098 0.0009873768
-0.0007421603 -0.0003873652 -0.0010365434
0.0005583760 0.0012251582 0.0006339280
0.0000869418 0.0003549072 -0.0006759036
0.0001409361 -0.0003918870 -0.0007182293
0.0014643318 0.0001198285 0.0014833106
-0.0003455558 -0.0005464685 0.0005691375
-0.0000951769 0.0005769488 -0.0009694491
-0.0019850731 0.0000833627 0.0014011041
-0.0002243268 0.0000071686 0.0001978542
-0.0000140946 0.0008803605 0.0003467160
0.0009180453 -0.0000205805 0.0001921299
0.0002326215 0.0004720817 0.0008967664
0.0009061050 -0.0008771595 -0.0005406529
0.0000296826 -0.0003165455 0.0016032775
0.0005653023 -0.0004270476 0.0016209415
0.0015923803 0.0018508712 0.0003735631
0.0011122442 -0.0000906278 0.0007790221
0.0001349027 -0.0010413688 0.0005172572
-0.0002512011 -0.0002185301 -0.0009096043
-0.0004609907 -0.0008471012 0.0005954164
0.0004049408 -0.0002540121 -0.0003031137
-0.0013334284 0.0002904444 -0.0000427043
-0.0000901368 0.0007974882 0.0006323092
0.0003344009 0.0003963514 -0.0000919052
&END VELOCITY
&KIND H
BASIS_SET DZVP-GTH
POTENTIAL GTH-BLYP-q1
&END KIND
&KIND O
BASIS_SET DZVP-GTH
POTENTIAL GTH-BLYP-q6
&END KIND
&END SUBSYS
&END FORCE_EVAL
&MOTION
&MD
ENSEMBLE NPT_I
STEPS 4000
TIMESTEP 0.5
TEMPERATURE 300.0
&BAROSTAT
PRESSURE 1.0132
TIMECON 100
&END BAROSTAT
&THERMOSTAT
&NOSE
LENGTH 3
YOSHIDA 3
TIMECON 100
MTS 2
&END NOSE
&END THERMOSTAT
&END MD
&PRINT
&TRAJECTORY
&EACH
MD 1
&END EACH
&END TRAJECTORY
&VELOCITIES
&EACH
MD 1
&END EACH
&END VELOCITIES
&END PRINT
&END MOTION
Hope this is enough to get some help.
thanks
tomaso
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