subject:"\[Pw_forum\] Langevin dynamics"

[Pw_forum] Langevin dynamics

2015-09-10 Thread Venkataramana Imandi

Dear Dr. Xiaochuan Ge

Thank you for intimating particularly about time step in the Langevin
dynamics. I tried with 2.D0 (0.1 fs), however, system is exploding. I tried
according to your suggestion 0.2D0 (0.01 fs), it is working. I am asking
you is there any possibility to do Langevin dynamics at higher timestep
e.g. 0.1 fs or 0.2 fs. If there such type of possibility, please inform me
as soon as possible and what parameters i have to alter in the input file
for doing Langevin dynamics at higher time step.

Once again thanks for remembering me about Langevin dynamics is successful
at small time step.

Best
Venkataramana Imandi
PhD student
IIT Bombay


Dear Venkataramana,

I have some experience using the Langevin code. ?Before we go further to
understand your problem, I would suggest you to significantly lower the dt
and try again. Please try dt=0.2 instead of 20. If it still does not work,
please let me know.

Best,

===
Dr. Xiaochuan Ge (Giovanni)
Center for Functional Nanomaterials
Brookhaven national laboratory
===
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Re: [Pw_forum] Langevin dynamics

2015-08-24 Thread Mahya Zare

Can anyone help me to make scf calculation input file in quantum espresso
for flat type single atom layer CeO2 nanosheet?

On Mon, Aug 24, 2015 at 6:08 PM, xiaochuan Ge  wrote:

>
> On 20 August 2015 at 00:40, Venkataramana Imandi <
> venkataramana.ima...@gmail.com> wrote:
>
>> Venkataramana
>
>
> Dear Venkataramana,
>
> I have some experience using the Langevin code. Before we go further to
> understand your problem, I would suggest you to significantly lower the dt
> and try again. Please try dt=0.2 instead of 20. If it still does not work,
> please let me know.
>
> Best, 
>
> ===
> Dr. Xiaochuan Ge (Giovanni)
> Center for Functional Nanomaterials
> Brookhaven national laboratory
> ===
>
> ___
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>
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Re: [Pw_forum] Langevin dynamics

2015-08-24 Thread xiaochuan Ge

On 20 August 2015 at 00:40, Venkataramana Imandi <
venkataramana.ima...@gmail.com> wrote:

> Venkataramana


Dear Venkataramana,

I have some experience using the Langevin code. Before we go further to
understand your problem, I would suggest you to significantly lower the dt
and try again. Please try dt=0.2 instead of 20. If it still does not work,
please let me know.

Best, 

===
Dr. Xiaochuan Ge (Giovanni)
Center for Functional Nanomaterials
Brookhaven national laboratory
===
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[Pw_forum] Langevin dynamics

2015-08-19 Thread Venkataramana Imandi

Dear Paolo Giannozzi sir,



Thank you sir for your kind reply and sorry for delaying reply. I felt same
thing while reading previous threads in pw_forum archives. According to
suggestions given by Ari Paavo Seitsonen sir, I made all corrections and
tried my level best. All trials lead to collapse of structure during
Langevin dynamics.

Best,
Venkataramana
PhD student
IIT Bombay

Langevin dynamics was implemented many years ago in QE, but I have never
heard of anybody using it, nor seen any evidence that it works (or that it
doesn't).

Paolo

On Mon, Aug 10, 2015 at 1:10 PM, Venkataramana Imandi
http://pwscf.org/mailman/listinfo/pw_forum>> wrote:



Dear Sir/ Madam,

I am using quantum espresso (version:5.1.2) for doing Langevin dynamics on
Ethene molecules were kept top and bottom of silver oxide surface (total
atoms: 37) running on Red Hat machine with serial and parallel process. In
the output file, the coordinates of some of the atoms getting starred(***).
In order to understand more about results, I tried with simple systems
containing 2 Si atoms, the results shows that Langevin dynamics is working
fine but the distance between two Si atoms goes on increasing (at the end
of 100 md steps, the distance is 560 Angstroms). Moreover, herein Langevin
dynamics is over-damped and the parameter of gamma (friction coefficient)
is not mentioned anywhere in the input file description of pw.x related
manual. Hence, I request you kindly suggest me how to perform Langevin
calculations on my original system. Input file and starred(**) coordinates
of my original system (output file) were attached.

 
calculation='md',
prefix='ag_eth',
dt=20.D0,
nstep=50,
  etot_conv_thr=1.0D-6,
   forc_conv_thr=1.0D-5,
   pseudo_dir = '/home/venkat/ORR1/PPS1'
 /

   ibrav=0,
nat=37,
ntyp=4,
  ecutwfc = 30.0,
nosym=.true.,
occupations='smearing',
smearing='m-p',
 degauss=0.03,
tot_charge=1.0
/

   electron_maxstep=2000,
  diagonalization='david',
   mixing_beta = 0.3,
conv_thr =  1.0D-6,
   scf_must_converge=.false.
/

pot_extrapolation = 'second_order',
wfc_extrapolation = 'second_order',
ion_dynamics='langevin',
tempw=300.D0,
nraise=1
 /
ATOMIC_SPECIES
C   12.0107 C.pbe-rrkjus.UPF
H   1.00794 H.pbe-rrkjus.UPF
O   15.9994 O.pbe-rrkjus.UPF
Ag 107.8682 Ag.pbe-d-rrkjus.UPF

CELL_PARAMETERS {angstrom}
7.898000 0.00 0.00
0.00 7.898000 0.00
0.00 0.00 9.747900

ATOMIC_POSITIONS {angstrom}

 C 3.674759 2.942993-3.493103
 H 4.121990 3.816735-4.007690
 H 4.121990 2.069251-4.007690
 C 2.211227 2.942993-3.493103
 H 1.763996 3.816735-4.007690
 H 1.763996 2.069251-4.007690
 O 0.00 0.00-2.719012
Ag 4.448147 4.449893-1.919012
Ag 4.448147 1.436093-1.919012
Ag 1.437838 4.449893-1.919012
Ag 1.437838 1.436093-1.919012
Ag 2.942993 2.942993 0.00
Ag 2.942993 0.00 0.00
Ag 0.00 2.942993 0.00
Ag 0.00 0.00 0.00
Ag 1.437838 1.436093 1.919012
Ag 1.437838 4.449893 1.919012
Ag 4.448147 1.436093 1.919012
Ag 4.448147 4.449893 1.919012
 O 0.00 0.00 2.719012
 C 3.674759 2.942993 3.493103
 H 4.121990 3.816735 4.007690
 H 4.121990 2.069251 4.007690
 C 2.211227 2.942993 3.493103
 H 1.763996 3.816735 4.007690
 H 1.763996 2.069251 4.007690
 O 0.00 5.885983-2.719012
Ag 2.942993 5.885983 0.00
Ag 0.00 5.885983 0.00
 O 0.00 5.885983 2.719012
 O 5.885983 0.00-2.719012
Ag 5.885983 2.942993 0.00
Ag 5.885983 0.00 0.00
 O 5.885983 0.00 2.719012
 O 5.885983 5.885983-2.719012
Ag 5.885983 5.885983 0.00
 O 5.885983 5.885983 2.719012

K_POINTS {gamma}

A BIT of OUTPUT FILE

ATOMIC_POSITIONS (angstrom)
C   23.936881089   5.854758432   2.384283563
H5.319738992   3.101932011  -2.806230409
H5.032723666   3.366896985  -3.263624443
C  -19.193958442  -0.839672619  -8.633281572
H2.840673809   3.320817821  -3.598829264
H2.259010092   3.506469010  -4.024573435
O3.200827481   3.891444136  -5.674056522
Ag  -2.799093034   8.698187934   0.392246441
Ag   6.216802688   0.615454519  -1.827886947
Ag  -1.094861601   5.714331653  -3.826763750
Ag

Re: [Pw_forum] Langevin dynamics

2015-08-15 Thread Paolo Giannozzi

Langevin dynamics was implemented many years ago in QE, but I have never
heard of anybody using it, nor seen any evidence that it works (or that it
doesn't).

Paolo

On Mon, Aug 10, 2015 at 1:10 PM, Venkataramana Imandi <
venkataramana.ima...@gmail.com> wrote:

> Dear Sir/ Madam,
>
> I am using quantum espresso (version:5.1.2) for doing Langevin dynamics on
> Ethene molecules were kept top and bottom of silver oxide surface (total
> atoms: 37) running on Red Hat machine with serial and parallel process. In
> the output file, the coordinates of some of the atoms getting starred(***).
> In order to understand more about results, I tried with simple systems
> containing 2 Si atoms, the results shows that Langevin dynamics is working
> fine but the distance between two Si atoms goes on increasing (at the end
> of 100 md steps, the distance is 560 Angstroms). Moreover, herein Langevin
> dynamics is over-damped and the parameter of gamma (friction coefficient)
> is not mentioned anywhere in the input file description of pw.x related
> manual. Hence, I request you kindly suggest me how to perform Langevin
> calculations on my original system. Input file and starred(**) coordinates
> of my original system (output file) were attached.
>
>  
> calculation='md',
> prefix='ag_eth',
> dt=20.D0,
> nstep=50,
>   etot_conv_thr=1.0D-6,
>forc_conv_thr=1.0D-5,
>pseudo_dir = '/home/venkat/ORR1/PPS1'
>  /
> 
>ibrav=0,
> nat=37,
> ntyp=4,
>   ecutwfc = 30.0,
> nosym=.true.,
> occupations='smearing',
> smearing='m-p',
>  degauss=0.03,
> tot_charge=1.0
> /
> 
>electron_maxstep=2000,
>   diagonalization='david',
>mixing_beta = 0.3,
> conv_thr =  1.0D-6,
>scf_must_converge=.false.
> /
> 
> pot_extrapolation = 'second_order',
> wfc_extrapolation = 'second_order',
> ion_dynamics='langevin',
> tempw=300.D0,
> nraise=1
>  /
> ATOMIC_SPECIES
> C   12.0107 C.pbe-rrkjus.UPF
> H   1.00794 H.pbe-rrkjus.UPF
> O   15.9994 O.pbe-rrkjus.UPF
> Ag 107.8682 Ag.pbe-d-rrkjus.UPF
>
> CELL_PARAMETERS {angstrom}
> 7.898000 0.00 0.00
> 0.00 7.898000 0.00
> 0.00 0.00 9.747900
>
> ATOMIC_POSITIONS {angstrom}
>
>  C 3.674759 2.942993-3.493103
>  H 4.121990 3.816735-4.007690
>  H 4.121990 2.069251-4.007690
>  C 2.211227 2.942993-3.493103
>  H 1.763996 3.816735-4.007690
>  H 1.763996 2.069251-4.007690
>  O 0.00 0.00-2.719012
> Ag 4.448147 4.449893-1.919012
> Ag 4.448147 1.436093-1.919012
> Ag 1.437838 4.449893-1.919012
> Ag 1.437838 1.436093-1.919012
> Ag 2.942993 2.942993 0.00
> Ag 2.942993 0.00 0.00
> Ag 0.00 2.942993 0.00
> Ag 0.00 0.00 0.00
> Ag 1.437838 1.436093 1.919012
> Ag 1.437838 4.449893 1.919012
> Ag 4.448147 1.436093 1.919012
> Ag 4.448147 4.449893 1.919012
>  O 0.00 0.00 2.719012
>  C 3.674759 2.942993 3.493103
>  H 4.121990 3.816735 4.007690
>  H 4.121990 2.069251 4.007690
>  C 2.211227 2.942993 3.493103
>  H 1.763996 3.816735 4.007690
>  H 1.763996 2.069251 4.007690
>  O 0.00 5.885983-2.719012
> Ag 2.942993 5.885983 0.00
> Ag 0.00 5.885983 0.00
>  O 0.00 5.885983 2.719012
>  O 5.885983 0.00-2.719012
> Ag 5.885983 2.942993 0.00
> Ag 5.885983 0.00 0.00
>  O 5.885983 0.00 2.719012
>  O 5.885983 5.885983-2.719012
> Ag 5.885983 5.885983 0.00
>  O 5.885983 5.885983 2.719012
>
> K_POINTS {gamma}
>
> A BIT of OUTPUT FILE
>
> ATOMIC_POSITIONS (angstrom)
> C   23.936881089   5.854758432   2.384283563
> H5.319738992   3.101932011  -2.806230409
> H5.032723666   3.366896985  -3.263624443
> C  -19.193958442  -0.839672619  -8.633281572
> H2.840673809   3.320817821  -3.598829264
> H2.259010092   3.506469010  -4.024573435
> O3.200827481   3.891444136  -5.674056522
> Ag  -2.799093034   8.698187934   0.392246441
> Ag   6.216802688   0.615454519  -1.827886947
> Ag  -1.094861601   5.714331653  -3.826763750
> Ag  -0.821908140  -7.523290040  -8.937996255
> Ag   7.394141127   8.391763262   7.199208896
> Ag  66.2293865871065.326804153 192.584344197
> Ag4515.057117298

[Pw_forum] Langevin dynamics

2015-08-10 Thread Venkataramana Imandi

Dear Sir/ Madam,

I am using quantum espresso (version:5.1.2) for doing Langevin dynamics on
Ethene molecules were kept top and bottom of silver oxide surface (total
atoms: 37) running on Red Hat machine with serial and parallel process. In
the output file, the coordinates of some of the atoms getting starred(***).
In order to understand more about results, I tried with simple systems
containing 2 Si atoms, the results shows that Langevin dynamics is working
fine but the distance between two Si atoms goes on increasing (at the end
of 100 md steps, the distance is 560 Angstroms). Moreover, herein Langevin
dynamics is over-damped and the parameter of gamma (friction coefficient)
is not mentioned anywhere in the input file description of pw.x related
manual. Hence, I request you kindly suggest me how to perform Langevin
calculations on my original system. Input file and starred(**) coordinates
of my original system (output file) were attached.

 
calculation='md',
prefix='ag_eth',
dt=20.D0,
nstep=50,
  etot_conv_thr=1.0D-6,
   forc_conv_thr=1.0D-5,
   pseudo_dir = '/home/venkat/ORR1/PPS1'
 /

   ibrav=0,
nat=37,
ntyp=4,
  ecutwfc = 30.0,
nosym=.true.,
occupations='smearing',
smearing='m-p',
 degauss=0.03,
tot_charge=1.0
/

   electron_maxstep=2000,
  diagonalization='david',
   mixing_beta = 0.3,
conv_thr =  1.0D-6,
   scf_must_converge=.false.
/

pot_extrapolation = 'second_order',
wfc_extrapolation = 'second_order',
ion_dynamics='langevin',
tempw=300.D0,
nraise=1
 /
ATOMIC_SPECIES
C   12.0107 C.pbe-rrkjus.UPF
H   1.00794 H.pbe-rrkjus.UPF
O   15.9994 O.pbe-rrkjus.UPF
Ag 107.8682 Ag.pbe-d-rrkjus.UPF

CELL_PARAMETERS {angstrom}
7.898000 0.00 0.00
0.00 7.898000 0.00
0.00 0.00 9.747900

ATOMIC_POSITIONS {angstrom}

 C 3.674759 2.942993-3.493103
 H 4.121990 3.816735-4.007690
 H 4.121990 2.069251-4.007690
 C 2.211227 2.942993-3.493103
 H 1.763996 3.816735-4.007690
 H 1.763996 2.069251-4.007690
 O 0.00 0.00-2.719012
Ag 4.448147 4.449893-1.919012
Ag 4.448147 1.436093-1.919012
Ag 1.437838 4.449893-1.919012
Ag 1.437838 1.436093-1.919012
Ag 2.942993 2.942993 0.00
Ag 2.942993 0.00 0.00
Ag 0.00 2.942993 0.00
Ag 0.00 0.00 0.00
Ag 1.437838 1.436093 1.919012
Ag 1.437838 4.449893 1.919012
Ag 4.448147 1.436093 1.919012
Ag 4.448147 4.449893 1.919012
 O 0.00 0.00 2.719012
 C 3.674759 2.942993 3.493103
 H 4.121990 3.816735 4.007690
 H 4.121990 2.069251 4.007690
 C 2.211227 2.942993 3.493103
 H 1.763996 3.816735 4.007690
 H 1.763996 2.069251 4.007690
 O 0.00 5.885983-2.719012
Ag 2.942993 5.885983 0.00
Ag 0.00 5.885983 0.00
 O 0.00 5.885983 2.719012
 O 5.885983 0.00-2.719012
Ag 5.885983 2.942993 0.00
Ag 5.885983 0.00 0.00
 O 5.885983 0.00 2.719012
 O 5.885983 5.885983-2.719012
Ag 5.885983 5.885983 0.00
 O 5.885983 5.885983 2.719012

K_POINTS {gamma}

A BIT of OUTPUT FILE

ATOMIC_POSITIONS (angstrom)
C   23.936881089   5.854758432   2.384283563
H5.319738992   3.101932011  -2.806230409
H5.032723666   3.366896985  -3.263624443
C  -19.193958442  -0.839672619  -8.633281572
H2.840673809   3.320817821  -3.598829264
H2.259010092   3.506469010  -4.024573435
O3.200827481   3.891444136  -5.674056522
Ag  -2.799093034   8.698187934   0.392246441
Ag   6.216802688   0.615454519  -1.827886947
Ag  -1.094861601   5.714331653  -3.826763750
Ag  -0.821908140  -7.523290040  -8.937996255
Ag   7.394141127   8.391763262   7.199208896
Ag  66.2293865871065.326804153 192.584344197
Ag4515.057117298 369.600932228 188.645687521
Ag 395.079974228 976.00510  23.641381229
Ag  -0.868373165   1.254442767  -0.725095564
Ag   0.598543920   4.290748028   1.130598433
Ag   3.451303546   0.003835176  -2.147641351
Ag   4.967046204   4.664900169   1.274377193
O4.154896086   3.538399188   4.404896973
C  399.041692489-175.281493613-563.071390643
H3.281002088   3.892508380   4.191590229
H5.590682748   1.083007852   4.528641700
C

[Pw_forum] Langevin dynamics

Re: [Pw_forum] Langevin dynamics

Re: [Pw_forum] Langevin dynamics

[Pw_forum] Langevin dynamics

Re: [Pw_forum] Langevin dynamics

[Pw_forum] Langevin dynamics

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