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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
メンテ
Page: [1]

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.
メンテ
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?
メンテ
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
メンテ
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.
メンテ

Page: [1]

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