[Pw_forum] Langevin dynamics
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 === ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Langevin dynamics
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 > === > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Langevin dynamics
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 === ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] Langevin dynamics
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. &control 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' / &system ibrav=0, nat=37, ntyp=4, ecutwfc = 30.0, nosym=.true., occupations='smearing', smearing='m-p', degauss=0.03, tot_charge=1.0 / &electrons electron_maxstep=2000, diagonalization='david', mixing_beta = 0.3, conv_thr = 1.0D-6, scf_must_converge=.false. / &ions 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 5.714
Re: [Pw_forum] Langevin dynamics
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. > > &control > 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' > / > &system >ibrav=0, > nat=37, > ntyp=4, > ecutwfc = 30.0, > nosym=.true., > occupations='smearing', > smearing='m-p', > degauss=0.03, > tot_charge=1.0 > / > &electrons >electron_maxstep=2000, > diagonalization='david', >mixing_beta = 0.3, > conv_thr = 1.0D-6, >scf_must_converge=.false. > / > &ions > 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 192.58434419
[Pw_forum] Langevin dynamics
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. &control 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' / &system ibrav=0, nat=37, ntyp=4, ecutwfc = 30.0, nosym=.true., occupations='smearing', smearing='m-p', degauss=0.03, tot_charge=1.0 / &electrons electron_maxstep=2000, diagonalization='david', mixing_beta = 0.3, conv_thr = 1.0D-6, scf_must_converge=.false. / &ions 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