Sudden changes of total energy and temperature

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lesheng
Posts: 10
Joined: Tue Feb 04, 2014 2:16 pm

Sudden changes of total energy and temperature

Post by lesheng »

Hi all,

I was trying to run a fpmd simulation with QBOX, the system is TiO2 anatase (101) surface with oxygen vacancy at the surface. However, during the simulation, there are several sudden changes of the total energy "etotal" and the ionic temperature "temp_ion" as shown in the following figures.
"total energy of run 1"
total energy of run 1
total energy of run 1
run1_etotal.jpg (102.02 KiB) Viewed 10336 times
"ionic temperature of run 1"
ionic temperature of run 1
ionic temperature of run 1
run1_temp.jpg (75.19 KiB) Viewed 10336 times
I thought maybe it is because the computation was not well converged (I am using version 1.52.3, there is no "scf_tol"), so I changed the number of scf iteration from 25 to 50, and I got the following result. The total energy and the ionic temperature (due to the figure limit of 3, I couldn't attach the temperature figure) still have some sudden changes as shown in the following figure.
"total energy of run 2"
total energy of run 2
total energy of run 2
run2_etotal.jpg (74.65 KiB) Viewed 10336 times
Here is the input file for my first run:

Code: Select all

load Vo1.qb_1.xml
reset_vcm
set xc PBE
set ecut 80.00000
set ecutprec 10
set wf_dyn PSDA
set wf_diag T
set nempty 203
run 0 1 2
constraint define position O1 O1
constraint define position O2 O2
constraint define position O3 O3
constraint define position O4 O4
constraint define position O5 O5
constraint define position O6 O6
constraint define position Ti1 Ti1
constraint define position Ti2 Ti2
constraint define position Ti3 Ti3
constraint define position Ti4 Ti4
constraint define position Ti5 Ti5
constraint define position Ti6 Ti6
constraint define position O7 O7
constraint define position O8 O8
constraint define position O9 O9
constraint define position O10 O10
constraint define position O11 O11
constraint define position O12 O12
constraint define position O13 O13
constraint define position O14 O14
constraint define position O15 O15
constraint define position O16 O16
constraint define position O17 O17
constraint define position O18 O18
constraint define position Ti7 Ti7
constraint define position Ti8 Ti8
constraint define position Ti9 Ti9
constraint define position Ti10 Ti10
constraint define position Ti11 Ti11
constraint define position Ti12 Ti12
constraint define position O19 O19
constraint define position O20 O20
constraint define position O21 O21
constraint define position O22 O22
constraint define position O23 O23
constraint define position O24 O24
constraint define position O25 O25
constraint define position O26 O26
constraint define position O27 O27
constraint define position O28 O28
constraint define position O29 O29
constraint define position O30 O30
constraint define position Ti13 Ti13
constraint define position Ti14 Ti14
constraint define position Ti15 Ti15
constraint define position Ti16 Ti16
constraint define position Ti17 Ti17
constraint define position Ti18 Ti18
constraint define position O31 O31
constraint define position O32 O32
constraint define position O33 O33
constraint define position O34 O34
constraint define position O35 O35
constraint define position O36 O36
constraint define position O37 O37
constraint define position O38 O38
constraint define position O39 O39
constraint define position O40 O40
constraint define position O41 O41
constraint define position O42 O42
constraint define position Ti19 Ti19
constraint define position Ti20 Ti20
constraint define position Ti21 Ti21
constraint define position Ti22 Ti22
constraint define position Ti23 Ti23
constraint define position Ti24 Ti24
constraint define position O43 O43
constraint define position O44 O44
constraint define position O45 O45
constraint define position O46 O46
constraint define position O47 O47
constraint define position O48 O48
set atoms_dyn MD
set NA_overlaps 16 17
set dt 20
set nempty 203
set thermostat SCALING
set th_time 100
set th_temp 295
run 600 25 2
save Vo1.md_600.xml
This is the input of the second run:

Code: Select all

load Vo1.qb_1.xml
reset_vcm
set xc PBE
set ecut 80.00000
set ecutprec 10
set wf_dyn PSDA
set wf_diag T
set nempty 203
run 0 1
constraint define position O1 O1
constraint define position O2 O2
constraint define position O3 O3
constraint define position O4 O4
constraint define position O5 O5
constraint define position O6 O6
constraint define position Ti1 Ti1
constraint define position Ti2 Ti2
constraint define position Ti3 Ti3
constraint define position Ti4 Ti4
constraint define position Ti5 Ti5
constraint define position Ti6 Ti6
constraint define position O7 O7
constraint define position O8 O8
constraint define position O9 O9
constraint define position O10 O10
constraint define position O11 O11
constraint define position O12 O12
constraint define position O13 O13
constraint define position O14 O14
constraint define position O15 O15
constraint define position O16 O16
constraint define position O17 O17
constraint define position O18 O18
constraint define position Ti7 Ti7
constraint define position Ti8 Ti8
constraint define position Ti9 Ti9
constraint define position Ti10 Ti10
constraint define position Ti11 Ti11
constraint define position Ti12 Ti12
constraint define position O19 O19
constraint define position O20 O20
constraint define position O21 O21
constraint define position O22 O22
constraint define position O23 O23
constraint define position O24 O24
constraint define position O25 O25
constraint define position O26 O26
constraint define position O27 O27
constraint define position O28 O28
constraint define position O29 O29
constraint define position O30 O30
constraint define position Ti13 Ti13
constraint define position Ti14 Ti14
constraint define position Ti15 Ti15
constraint define position Ti16 Ti16
constraint define position Ti17 Ti17
constraint define position Ti18 Ti18
constraint define position O31 O31
constraint define position O32 O32
constraint define position O33 O33
constraint define position O34 O34
constraint define position O35 O35
constraint define position O36 O36
constraint define position O37 O37
constraint define position O38 O38
constraint define position O39 O39
constraint define position O40 O40
constraint define position O41 O41
constraint define position O42 O42
constraint define position Ti19 Ti19
constraint define position Ti20 Ti20
constraint define position Ti21 Ti21
constraint define position Ti22 Ti22
constraint define position Ti23 Ti23
constraint define position Ti24 Ti24
constraint define position O43 O43
constraint define position O44 O44
constraint define position O45 O45
constraint define position O46 O46
constraint define position O47 O47
constraint define position O48 O48
set atoms_dyn MD
set NA_overlaps 16 17
set dt 20
set nempty 203
set thermostat SCALING
set th_time 100
set th_temp 295
run 300 50 2
save Vo1.md_300.xml
Before I ran the md simulation, the structure was optimized with Quantum Espresso and the ground state was well converged with QBOX.

In addition, when I check the trajectory of the simulation (for the first run), the atoms will "fly away" from the fixed layers slowly along Z direction to the vacuum.

I had suffered from this for a very long time, and I have totally no idea what is going on. If anyone could give me some suggestion, that would be great.

Thanks,
Lesheng Li
Lesheng Li
Ph.D Candidate
Chemistry Department
University of North Carolina at Chapel Hill
Top
lesheng
Posts: 10
Joined: Tue Feb 04, 2014 2:16 pm

Re: Sudden changes of total energy and temperature

Post by lesheng »

Update:

I checked the energy gap of this system, which sometimes goes to zero at the sudden change points (CBM and VBM cross sometimes). I suspect this could be the problem that makes the system more metallic and get difficult to get converged. I'll use fermi_temp keyword and hope this could work.

Thanks,
lesheng li
lesheng wrote:Hi all,

I was trying to run a fpmd simulation with QBOX, the system is TiO2 anatase (101) surface with oxygen vacancy at the surface. However, during the simulation, there are several sudden changes of the total energy "etotal" and the ionic temperature "temp_ion" as shown in the following figures.
"total energy of run 1"
run1_etotal.jpg
"ionic temperature of run 1"
run1_temp.jpg
I thought maybe it is because the computation was not well converged (I am using version 1.52.3, there is no "scf_tol"), so I changed the number of scf iteration from 25 to 50, and I got the following result. The total energy and the ionic temperature (due to the figure limit of 3, I couldn't attach the temperature figure) still have some sudden changes as shown in the following figure.
"total energy of run 2"
run2_etotal.jpg
Here is the input file for my first run:

Code: Select all

load Vo1.qb_1.xml
reset_vcm
set xc PBE
set ecut 80.00000
set ecutprec 10
set wf_dyn PSDA
set wf_diag T
set nempty 203
run 0 1 2
constraint define position O1 O1
constraint define position O2 O2
constraint define position O3 O3
constraint define position O4 O4
constraint define position O5 O5
constraint define position O6 O6
constraint define position Ti1 Ti1
constraint define position Ti2 Ti2
constraint define position Ti3 Ti3
constraint define position Ti4 Ti4
constraint define position Ti5 Ti5
constraint define position Ti6 Ti6
constraint define position O7 O7
constraint define position O8 O8
constraint define position O9 O9
constraint define position O10 O10
constraint define position O11 O11
constraint define position O12 O12
constraint define position O13 O13
constraint define position O14 O14
constraint define position O15 O15
constraint define position O16 O16
constraint define position O17 O17
constraint define position O18 O18
constraint define position Ti7 Ti7
constraint define position Ti8 Ti8
constraint define position Ti9 Ti9
constraint define position Ti10 Ti10
constraint define position Ti11 Ti11
constraint define position Ti12 Ti12
constraint define position O19 O19
constraint define position O20 O20
constraint define position O21 O21
constraint define position O22 O22
constraint define position O23 O23
constraint define position O24 O24
constraint define position O25 O25
constraint define position O26 O26
constraint define position O27 O27
constraint define position O28 O28
constraint define position O29 O29
constraint define position O30 O30
constraint define position Ti13 Ti13
constraint define position Ti14 Ti14
constraint define position Ti15 Ti15
constraint define position Ti16 Ti16
constraint define position Ti17 Ti17
constraint define position Ti18 Ti18
constraint define position O31 O31
constraint define position O32 O32
constraint define position O33 O33
constraint define position O34 O34
constraint define position O35 O35
constraint define position O36 O36
constraint define position O37 O37
constraint define position O38 O38
constraint define position O39 O39
constraint define position O40 O40
constraint define position O41 O41
constraint define position O42 O42
constraint define position Ti19 Ti19
constraint define position Ti20 Ti20
constraint define position Ti21 Ti21
constraint define position Ti22 Ti22
constraint define position Ti23 Ti23
constraint define position Ti24 Ti24
constraint define position O43 O43
constraint define position O44 O44
constraint define position O45 O45
constraint define position O46 O46
constraint define position O47 O47
constraint define position O48 O48
set atoms_dyn MD
set NA_overlaps 16 17
set dt 20
set nempty 203
set thermostat SCALING
set th_time 100
set th_temp 295
run 600 25 2
save Vo1.md_600.xml
This is the input of the second run:

Code: Select all

load Vo1.qb_1.xml
reset_vcm
set xc PBE
set ecut 80.00000
set ecutprec 10
set wf_dyn PSDA
set wf_diag T
set nempty 203
run 0 1
constraint define position O1 O1
constraint define position O2 O2
constraint define position O3 O3
constraint define position O4 O4
constraint define position O5 O5
constraint define position O6 O6
constraint define position Ti1 Ti1
constraint define position Ti2 Ti2
constraint define position Ti3 Ti3
constraint define position Ti4 Ti4
constraint define position Ti5 Ti5
constraint define position Ti6 Ti6
constraint define position O7 O7
constraint define position O8 O8
constraint define position O9 O9
constraint define position O10 O10
constraint define position O11 O11
constraint define position O12 O12
constraint define position O13 O13
constraint define position O14 O14
constraint define position O15 O15
constraint define position O16 O16
constraint define position O17 O17
constraint define position O18 O18
constraint define position Ti7 Ti7
constraint define position Ti8 Ti8
constraint define position Ti9 Ti9
constraint define position Ti10 Ti10
constraint define position Ti11 Ti11
constraint define position Ti12 Ti12
constraint define position O19 O19
constraint define position O20 O20
constraint define position O21 O21
constraint define position O22 O22
constraint define position O23 O23
constraint define position O24 O24
constraint define position O25 O25
constraint define position O26 O26
constraint define position O27 O27
constraint define position O28 O28
constraint define position O29 O29
constraint define position O30 O30
constraint define position Ti13 Ti13
constraint define position Ti14 Ti14
constraint define position Ti15 Ti15
constraint define position Ti16 Ti16
constraint define position Ti17 Ti17
constraint define position Ti18 Ti18
constraint define position O31 O31
constraint define position O32 O32
constraint define position O33 O33
constraint define position O34 O34
constraint define position O35 O35
constraint define position O36 O36
constraint define position O37 O37
constraint define position O38 O38
constraint define position O39 O39
constraint define position O40 O40
constraint define position O41 O41
constraint define position O42 O42
constraint define position Ti19 Ti19
constraint define position Ti20 Ti20
constraint define position Ti21 Ti21
constraint define position Ti22 Ti22
constraint define position Ti23 Ti23
constraint define position Ti24 Ti24
constraint define position O43 O43
constraint define position O44 O44
constraint define position O45 O45
constraint define position O46 O46
constraint define position O47 O47
constraint define position O48 O48
set atoms_dyn MD
set NA_overlaps 16 17
set dt 20
set nempty 203
set thermostat SCALING
set th_time 100
set th_temp 295
run 300 50 2
save Vo1.md_300.xml
Before I ran the md simulation, the structure was optimized with Quantum Espresso and the ground state was well converged with QBOX.

In addition, when I check the trajectory of the simulation (for the first run), the atoms will "fly away" from the fixed layers slowly along Z direction to the vacuum.

I had suffered from this for a very long time, and I have totally no idea what is going on. If anyone could give me some suggestion, that would be great.

Thanks,
Lesheng Li
Lesheng Li
Ph.D Candidate
Chemistry Department
University of North Carolina at Chapel Hill
Top
fgygi
Site Admin
Posts: 167
Joined: Tue Jun 17, 2008 7:03 pm

Re: Sudden changes of total energy and temperature

Post by fgygi »

Hi Lesheng,
It is likely that the reason you mention in your update is the cause of the problem.
However, from the input file, I see that you are not using the official version of Qbox from the http://qboxcode.org distribution site. If you are using an unofficial modified version, we are unfortunately unable to help. Furthermore, it seems that you are using a very old version (although the version numbers of unofficial versions are not significant). I encourage you to download and install the most recent official version (1.62.7) which has many more features. We can help in the installation process if needed.
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