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Temperature fluctations in NVT Nose Hoover MD calculations Date: 2021/07/20 12:08 Name: Lovleen Kaur   <lovleenkaurkkr@gmail.com> Dear OpenMX Developers, I am trying to do NVT MD calculations using Nose Hoover thermostat in order to check the stability of armchair graphene nanoribbon. I have run this calculation starting from 1 femtosecond to 1 picosecond at a constant temperature of 300K. As NVT is a constant temperature MD, so temperature is supposed to be constant during the calculations, but in my case temperature changes a lot for example it goes from 300K to 160K. What could be reason for such fluctuations in the temperature. The input file of my calculations is given below. &#65279;# # This was generated by OpenMX Viewer System.CurrrentDirectory ./ System.Name graphene DATA.PATH ../../../../../DFT_DATA13 level.of.stdout 1 level.of.fileout 1 Species.Number 4 <Definition.of.Atomic.Species H H6.0-s2p1 H_PBE13 C C6.0-s2p2d1 C_PBE13 Fe Fe8.0S-s2p2d1 Fe_PBE13S O O6.0-s2p2d1 O_PBE13 Definition.of.Atomic.Species> Atoms.Number 140 Atoms.SpeciesAndCoordinates.Unit Ang <Atoms.SpeciesAndCoordinates 1 C 0.68427000 0.94239000 0.10502000 2.00000 2.0000 2 C 2.06147000 0.94135000 0.09965000 2.00000 2.0000 3 C 5.00123000 0.93902000 0.00057000 2.00000 2.0000 4 C 9.31222000 0.95118000 -0.25382000 2.00000 2.0000 5 C 6.37758000 0.94076000 -0.04988000 2.00000 2.0000 6 C 10.68825000 0.95638000 -0.27455000 2.00000 2.0000 7 C -0.06102000 2.14286000 0.03231000 2.00000 2.0000 8 C -0.06676000 4.61081000 -0.09058000 2.00000 2.0000 9 C -0.06520000 7.06685000 -0.22764000 2.00000 2.0000 10 C -0.05797000 9.53072000 -0.41083000 2.00000 2.0000 11 C 2.80537000 2.14141000 0.02367000 2.00000 2.0000 12 C 2.81113000 4.60953000 -0.08894000 2.00000 2.0000 13 C 2.81142000 7.06751000 -0.21512000 2.00000 2.0000 14 C 2.80583000 9.53191000 -0.37925000 2.00000 2.0000 15 C 0.65426000 3.37197000 -0.02786000 2.00000 2.0000 16 C 0.65195000 5.83846000 -0.15723000 2.00000 2.0000 17 C 0.65628000 8.30311000 -0.31558000 2.00000 2.0000 18 C 0.68766000 10.72919000 -0.51065000 2.00000 2.0000 19 C 2.09054000 3.37075000 -0.02968000 2.00000 2.0000 20 C 2.09349000 5.83847000 -0.15413000 2.00000 2.0000 21 C 2.09083000 8.30412000 -0.30438000 2.00000 2.0000 22 C 2.06362000 10.73020000 -0.49368000 2.00000 2.0000 23 C 4.25358000 2.14014000 -0.00598000 2.00000 2.0000 24 C 4.24226000 4.61005000 -0.08680000 2.00000 2.0000 25 C 4.24249000 7.07075000 -0.18959000 2.00000 2.0000 26 C 4.25013000 9.53575000 -0.31823000 2.00000 2.0000 27 C 8.56776000 2.14973000 -0.15488000 2.00000 2.0000 28 C 8.55706000 4.62048000 -0.06881000 2.00000 2.0000 29 C 8.54530000 7.08329000 0.02652000 2.00000 2.0000 30 C 8.53982000 9.55999000 0.15840000 2.00000 2.0000 31 C 7.12072000 2.14319000 -0.09974000 2.00000 2.0000 32 C 7.12557000 4.61571000 -0.09541000 2.00000 2.0000 33 C 7.11575000 7.07501000 -0.07653000 2.00000 2.0000 34 C 7.11038000 9.54617000 -0.07733000 2.00000 2.0000 35 C 11.42956000 2.15784000 -0.18767000 2.00000 2.0000 36 C 11.43716000 4.62377000 -0.02500000 2.00000 2.0000 37 C 11.42759000 7.07822000 0.26321000 2.00000 2.0000 38 Fe 11.41590000 9.56462000 1.44941000 7.00000 7.0000 39 C 4.96599000 3.37093000 -0.05463000 2.00000 2.0000 40 C 4.96120000 5.84142000 -0.12857000 2.00000 2.0000 41 C 4.96489000 8.30979000 -0.21686000 2.00000 2.0000 42 C 4.99486000 10.73777000 -0.33972000 2.00000 2.0000 43 C 9.27974000 3.38163000 -0.10869000 2.00000 2.0000 44 C 9.27156000 5.85142000 0.01340000 2.00000 2.0000 45 C 9.24817000 8.31385000 0.21862000 2.00000 2.0000 46 C 9.23041000 10.79413000 0.32080000 2.00000 2.0000 47 C 6.40445000 3.37437000 -0.08537000 2.00000 2.0000 48 C 6.40470000 5.84562000 -0.10889000 2.00000 2.0000 49 C 6.39713000 8.31283000 -0.12537000 2.00000 2.0000 50 C 6.36441000 10.74259000 -0.21278000 2.00000 2.0000 51 C 10.71597000 3.38606000 -0.11145000 2.00000 2.0000 52 C 10.71702000 5.85244000 0.07296000 2.00000 2.0000 53 C 10.65712000 8.27060000 0.49910000 2.00000 2.0000 54 C 10.55762000 10.90951000 0.68044000 2.00000 2.0000 55 H 0.17046000 -0.01493000 0.16469000 0.50000 0.5000 56 H 2.57610000 -0.01574000 0.15476000 0.50000 0.50000 57 H 4.48866000 -0.01984000 0.03849000 0.50000 0.50000 58 H 6.89501000 -0.01641000 -0.04259000 0.50000 0.50000 59 H 8.79780000 -0.00488000 -0.32456000 0.50000 0.50000 60 H 11.20505000 0.00277000 -0.35761000 0.50000 0.50000 61 H 11.04617000 11.89737000 0.64341000 0.50000 0.50000 62 H 8.68122000 11.72106000 0.14493000 0.50000 0.50000 63 H 6.87423000 11.70306000 -0.21394000 0.50000 0.50000 64 H 4.48453000 11.69339000 -0.43872000 0.50000 0.50000 65 H 2.57921000 11.68563000 -0.56419000 0.50000 0.50000 66 H 0.17378000 11.68455000 -0.59381000 0.50000 0.50000 67 C 13.61959000 0.95698000 -0.21396000 2.00000 2.0000 68 C 14.99437000 0.95348000 -0.17049000 2.00000 2.0000 69 C 17.92548000 0.94527000 0.01326000 2.00000 2.0000 70 C 19.30199000 0.94356000 0.04752000 2.00000 2.0000 71 C 12.87607000 2.16012000 -0.16944000 2.00000 2.0000 72 C 12.86782000 4.63086000 -0.02387000 2.00000 2.0000 73 C 12.87569000 7.09410000 0.21923000 2.00000 2.0000 74 C 12.98637000 9.57332000 0.56595000 2.00000 2.0000 75 C 15.73864000 2.15450000 -0.09850000 2.00000 2.0000 76 C 15.74812000 4.62667000 -0.07120000 2.00000 2.0000 77 C 15.75847000 7.08161000 -0.02402000 2.00000 2.0000 78 C 15.76659000 9.55223000 -0.00404000 2.00000 2.0000 79 C 13.58918000 3.39058000 -0.09465000 2.00000 2.0000 80 C 13.58720000 5.86458000 0.05014000 2.00000 2.0000 81 C 13.62651000 8.32777000 0.28911000 2.00000 2.0000 82 C 13.70526000 10.78126000 0.41544000 2.00000 2.0000 83 C 15.02612000 3.38706000 -0.08541000 2.00000 2.0000 84 C 15.03229000 5.85749000 -0.01527000 2.00000 2.0000 85 C 15.04821000 8.32317000 0.07929000 2.00000 2.0000 86 C 15.05344000 10.76752000 0.13184000 2.00000 2.0000 87 C 17.18617000 2.14918000 -0.05057000 2.00000 2.0000 88 C 17.18051000 4.61964000 -0.08466000 2.00000 2.0000 89 C 17.18830000 7.07659000 -0.10748000 2.00000 2.0000 90 C 17.19789000 9.54242000 -0.19576000 2.00000 2.0000 91 C 20.04990000 2.14364000 0.01186000 2.00000 2.0000 92 C 20.06226000 4.61218000 -0.09105000 2.00000 2.0000 93 C 20.06420000 7.06868000 -0.21178000 2.00000 2.0000 94 C 20.05625000 9.53232000 -0.38873000 2.00000 2.0000 95 C 17.90167000 3.37811000 -0.06282000 2.00000 2.0000 96 C 17.90355000 5.84604000 -0.11015000 2.00000 2.0000 97 C 17.91105000 8.31134000 -0.19075000 2.00000 2.0000 98 C 17.93703000 10.73746000 -0.36602000 2.00000 2.0000 99 C 19.33811000 3.37507000 -0.04474000 2.00000 2.0000 100 C 19.34521000 5.84180000 -0.13720000 2.00000 2.0000 101 C 19.34319000 8.30711000 -0.26836000 2.00000 2.0000 102 C 19.30922000 10.73169000 -0.46493000 2.00000 2.0000 103 H 13.10406000 0.00131000 -0.27766000 0.50000 0.50000 104 H 15.51016000 -0.00370000 -0.20669000 0.50000 0.50000 105 H 17.40788000 -0.01130000 0.04301000 0.50000 0.50000 106 H 19.81298000 -0.01578000 0.09882000 0.50000 0.50000 107 H 19.81906000 11.68441000 -0.59382000 0.50000 0.50000 108 H 17.41937000 11.69270000 -0.42205000 0.50000 0.50000 109 H 15.57645000 11.71862000 0.05125000 0.50000 0.50000 110 H 13.19933000 11.73702000 0.55429000 0.50000 0.50000 111 H 8.37571000 9.35851000 2.85320000 0.50000 0.50000 112 H 8.64148000 7.94703000 3.47040000 0.50000 0.50000 113 O 12.83728000 7.84003000 4.60020000 3.00000 3.00000 114 H 13.06195000 6.99170000 4.10591000 0.50000 0.50000 115 H 12.39050000 7.53694000 5.40682000 0.50000 0.50000 116 O 6.08188000 4.98945000 3.03258000 3.00000 3.00000 117 H 5.51502000 5.53210000 2.45501000 0.50000 0.50000 118 H 6.23625000 4.19449000 2.49077000 0.50000 0.50000 119 O 12.04731000 6.53452000 -3.00834000 3.00000 3.00000 120 H 11.30271000 6.19433000 -2.48191000 0.50000 0.50000 121 H 12.46375000 7.17320000 -2.40295000 0.50000 0.50000 122 O 5.59118000 4.60497000 -3.31456000 3.00000 3.00000 123 H 5.06967000 5.15609000 -2.70795000 0.50000 0.50000 124 H 6.12627000 4.06633000 -2.70850000 0.50000 0.50000 125 O 13.31544000 5.56439000 3.32276000 3.00000 3.00000 126 H 14.21277000 5.14102000 3.30163000 0.50000 0.50000 127 H 13.07949000 5.65461000 2.38297000 0.50000 0.50000 128 O 14.02602000 4.44079000 -3.31580000 3.00000 3.00000 129 H 13.32888000 5.12808000 -3.23411000 0.50000 0.50000 130 H 13.76670000 3.77305000 -2.66228000 0.50000 0.50000 131 O 8.55124000 6.28779000 3.24338000 3.00000 3.00000 132 H 8.95208000 6.07957000 2.38104000 0.50000 0.50000 133 H 7.66261000 5.84967000 3.20365000 0.50000 0.50000 134 O 11.31259000 9.52821000 3.37302000 3.00000 3.00000 135 H 11.91226000 8.83210000 3.83232000 0.50000 0.50000 136 H 10.33902000 9.27241000 3.56607000 0.50000 0.50000 137 O 15.75204000 4.24770000 3.11438000 3.00000 3.00000 138 H 16.33937000 4.78411000 2.55177000 0.50000 0.50000 139 H 15.54813000 3.48752000 2.53957000 0.50000 0.50000 140 O 8.78442000 8.92983000 3.62588000 3.00000 3.00000 Atoms.SpeciesAndCoordinates> Atoms.UnitVectors.Unit Ang <Atoms.UnitVectors 21.56071 -0.00046 -0.00320 -0.00030 29.97207 0.00941 -0.00230 0.00943 30.00598 Atoms.UnitVectors> scf.XcType GGA-PBE scf.SpinPolarization on scf.ElectronicTemperature 300.0 scf.energycutoff 250.0 scf.maxIter 100 scf.EigenvalueSolver band scf.Kgrid 5 1 1 scf.Mixing.Type rmm-diisk scf.Init.Mixing.Weight 0.05 scf.Min.Mixing.Weight 0.01 scf.Max.Mixing.Weight 0.30 scf.Mixing.History 25 scf.Mixing.StartPulay 15 scf.criterion 1.0e-7 # # vdW # scf.dftD on version.dftD 3 DFTD3.damp bj DFTD.IntDirection 0 0 0 DFT.scale6 1.0 DFT.scale8 0.7875 DFTD.a1 0.4289 DFT.a2 4.4407 # # MD or Geometry Optimization # MD.Type NVT_NH # Nomd|Constant_Energy_MD|Opt MD.maxIter 5000 # default=1 MD.TimeStep 1 # default=0.5 (fs) MD.Opt.criterion 2.0e-4 # default=1.0e-4 (Hartree/bohr) MD.Opt.DIIS_Mixing 0.1 # default=0.5 <MD.TempControl 1 5000 300.0 MD.TempControl> NH.Mass.HeatBath 1 Regards, Lovleen Kaur

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Re: Temperature fluctations in NVT Nose Hoover MD calculations ( No.1 ) Date: 2021/07/20 15:40 Name: Pavel Ondracka  <pavel.ondracka@email.cz> This is expected, see for example the MD temperature plots in the manual http://www.openmx-square.org/openmx_man3.9/node60.html There are two reasons: 1) In general the temperature IS always supposed to fluctuate. This is basic thermodynamics, the more particles you have the smaller the fluctuations will be, IIRC the relative fluctuations should be approximately as 1/sqrt(n) (you can probably find better in some basic thermodynamics textbook). 2) The thermostat takes some time to stabilize at the beginning (this is especially the case if you have some potential energy stored in the system, i.e. some residual forces), so at the beginning the temperature will fluctuate even more, see again the Figure 12b from the previous link. How fast the temperature stabilizes depends on the heat bath mass (NH.Mass.HeatBath) settings, search some recent forum posts about how to set it properly. It is important to set it properly, too small values may cause (unphysical) high-frequency temperature oscillations, too high values will lead to a bad (slow) temperature control. Maybe "NH.Mass.HeatBath 1" for 140 atoms is not so good value. Re: Temperature fluctations in NVT Nose Hoover MD calculations ( No.2 ) Date: 2021/07/20 16:49 Name: Lovleen Kaur  <lovleenkaurkkr@gmail.com> Dear Pavel Ondracka Thank you for your response. Can you suggest me that what would be the appropriate value of NH.Mass.HeatBath for my system? Re: Temperature fluctations in NVT Nose Hoover MD calculations ( No.3 ) Date: 2021/07/20 16:59 Name: Pavel Ondracka  <pavel.ondracka@email.cz> I believe this was already answered in http://www.openmx-square.org/forum/patio.cgi?mode=view&no=2703 Re: Temperature fluctations in NVT Nose Hoover MD calculations ( No.4 ) Date: 2021/07/20 17:27 Name: Lovleen Kaur  <lovleenkaurkkr@gmail.com> Yes, it is there in http://www.openmx-square.org/forum/patio.cgi?mode=view&no=2703 But i am not getting the value of "t" for my system that is given in the formula.

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