From c77f4f828b4f6193f1acdb57f8ae6379635ae601 Mon Sep 17 00:00:00 2001 From: Timur Bazhirov Date: Tue, 13 Oct 2020 11:25:09 -0700 Subject: [PATCH 01/16] Minor clarification --- README.md | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index a47f675a..596d96fb 100644 --- a/README.md +++ b/README.md @@ -25,11 +25,10 @@ See [dev branch](https://github.com/Exabyte-io/rewotes/tree/dev) also. ## Notes -Examples listed here are only meant as guidelines and do not necessarily reflect on the type of work to be performed at the company. +Examples listed here are only meant as guidelines and do not necessarily reflect on the type of work to be performed at the company. Modifications to the individual assignments with an advance notice are encouraged. -Modifications to the individual assignments with an advance notice are encouraged. Candidates are free to share the results. +We will screen for the ability to (1) pick up new concepts quickly, (2) implement a working proof-of-concept solution, and (3) outline how the PoC can become more mature. We value attention to details and modularity. -We will screen for the ability to pick up new concepts quickly and implement a working solution. We value attention to details and modularity. ## Hiring process From 3b1e60c9947b41d20503211df00e048d28db3ef7 Mon Sep 17 00:00:00 2001 From: tjduigna Date: Mon, 28 Mar 2022 14:18:10 -0700 Subject: [PATCH 02/16] feat: app infra rewote --- Application-Infrastructure.md | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 Application-Infrastructure.md diff --git a/Application-Infrastructure.md b/Application-Infrastructure.md new file mode 100644 index 00000000..9e738a34 --- /dev/null +++ b/Application-Infrastructure.md @@ -0,0 +1,35 @@ +# Application Infrastructure (DevOps) + +> Ideal candidate: skilled software engineer versed in application infrastructure and DevOps + +# Overview + +The aim of this task is to create a simple application package (either python or javascript) that includes +complete application testing infrastructure as well as a complete CICD solution using Github workflows. + +# Requirements + +1. A non-trivial application, e.g. a Flask server with a UI or a React app with a UI with testable components +2. An appropriate end-to-end testing framework implementation (e.g. Cypress) for the application +3. An automated workflow using Github actions to verify that the tests pass + +# Expectations + +- The application may be relatively simple, this is focused more on application infrastructure and DevOps, but the tests must actually verify functionality +- Correctly passes the tests in automation and displays coverage metrics +- Clean workflow logic + +# Timeline + +We leave exact timing to the candidate. Must fit Within 5 days total. + +# User story + +As a developer of this application I can: + +- view important coverage metrics of my application +- be aware of the number of tests running/passing when developing + +# Notes + +- Commit early and often From 75ea0c25be82b90dd366d5d8df51f200f1da5888 Mon Sep 17 00:00:00 2001 From: Timur Bazhirov Date: Fri, 1 Apr 2022 15:10:57 -0700 Subject: [PATCH 03/16] feat: rename file --- Application-Infrastructure.md => End-to-End-Tests.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename Application-Infrastructure.md => End-to-End-Tests.md (96%) diff --git a/Application-Infrastructure.md b/End-to-End-Tests.md similarity index 96% rename from Application-Infrastructure.md rename to End-to-End-Tests.md index 9e738a34..1b4d3d1e 100644 --- a/Application-Infrastructure.md +++ b/End-to-End-Tests.md @@ -1,4 +1,4 @@ -# Application Infrastructure (DevOps) +# End-to-end Tests (DevOps) > Ideal candidate: skilled software engineer versed in application infrastructure and DevOps From 4cbf3eae3554835d3ca1968905bac95dadca0093 Mon Sep 17 00:00:00 2001 From: Timur Bazhirov Date: Fri, 1 Apr 2022 15:11:16 -0700 Subject: [PATCH 04/16] feat: add cloud infrastructure / HPC rewote --- Cloud-Infrastructure.md | 42 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 Cloud-Infrastructure.md diff --git a/Cloud-Infrastructure.md b/Cloud-Infrastructure.md new file mode 100644 index 00000000..1a8aad0c --- /dev/null +++ b/Cloud-Infrastructure.md @@ -0,0 +1,42 @@ +# Cloud Infrastructure (HPC/DevOps) + +> Ideal candidate: skilled HPC engineer versed in cloud, HPC, and DevOps + +# Overview + +The aim of this task is to create a CI/CD pipeline (github workflow) that includes (i) deploying cloud infrastructure for cluster compute, (ii) configuring it for running HPC application(s), and (iii) running benchmarks for a set of distributed memory calculations. + +# Requirements + +1. A working CI/CD pipeline - e.g. GitHub workflow - able to deploy and configure an HPC cluster +2. An automated workflow (using a configurable Github action) to benchmark one or more HPC application on one or more cloud instance type + +# Expectations + +- The application may be relatively simple - e.g. Linpack, this is focused more on application infrastructure and DevOps, but the tests must actually verify functionality +- Correctly passes the tests in automation and displays coverage metrics +- Clean workflow logic + +# Timeline + +We leave exact timing to the candidate. Should fit Within 5 days total. + +# User story + +As a user of this CI/CD pipelin I can: + +- initiate tests for a specific number of scenarios: e.g. 2 nodes, 16 core per node +- select the instance type to be used + +# Notes + +- Commit early and often + +# Suggestions + +We suggest: + +- using AWS as the cloud provider +- using Exabench as the source of benchmarks: https://github.com/Exabyte-io/exabyte-benchmarks-suite +- using CentOS or similar as operating system +- using Terraform for infrastructure management From 9c83e4ae9e4751db14fb6ac8994b21d4dac62e7a Mon Sep 17 00:00:00 2001 From: Timur Bazhirov Date: Fri, 1 Apr 2022 15:19:04 -0700 Subject: [PATCH 05/16] feat: updated readme --- README.md | 26 +++++++++++++++++++------- 1 file changed, 19 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index 596d96fb..1b84b0ad 100644 --- a/README.md +++ b/README.md @@ -10,6 +10,17 @@ We find that regular job interview questions can often be misleading and so use Each file represents an assignment similar to what one would get when hired. +| Focus | ReWote | Notes | +| ---------------| --------------------------| ------------------------------ | +| Comp. Science | [Convergence Tracker](Basis-Set-Selector.md) | | +| Comp. Science | [Basis Set Selector](Convergence-Tracker.md) | | +| Data. Science | [ML Property Predict](ML-Band-Gaps.md) | | +| Front-End / UX | [Materials Designer](Materials-Designer.md) | | +| Front-End / UX | [Flowchart Designer](Flowchart-Designer.md) | | +| Back-End / Ops | [Parallel Uploader](Flowchart-Designer.md) | | +| CI/CD, DevOps | [End-to-End Tests](Flowchart-Designer.md) | | +| HPC, Cloud Inf | [Cloud HPC Bench.](Flowchart-Designer.md) | | + ## Usage We suggest the following flow: @@ -36,18 +47,19 @@ Our hiring process in more details: | Stage | Target Duration | Topic | | ----------------- | ----------------- | ------------------------------ | -| 0. Email screen | | why exabyte.io | +| 0. Email screen | | why mat3ra.com / exabyte.io | | 1. Phone screen | 15-20 min | career goals, basic skillset | -| 2. ReWoTe | 1-2h x 1-5 days | real-world work/thought process| -| 3. On-site meet | 2-4 x 30 min | personality fit | +| 2. ReWoTe | 1-2h x 2-5 days | real-world work/thought process| +| 3. On-site meet | 3-4 x 30 min | personality fit | | 4. Discuss offer | 30 min | cash/equity/benefits | -| 5. Decision | | when to start | +| 5. References | 2 x 15 min | sanity check | +| 6. Decision | | when to start | -TOTAL: ~2 weeks tentative +TOTAL: ~2 weeks tentative. ## Contact info -With any questions about this repository or our hiring process please contact us at info@exabyte.io. +With any questions about this repository or our hiring process please contact us at info@mat3ra.com. -© 2020 Exabyte Inc. +© 2022 Exabyte Inc. From b91eeffabaed5f5c8e2222ef9451e4b18d74751a Mon Sep 17 00:00:00 2001 From: Timur Bazhirov Date: Fri, 1 Apr 2022 15:30:05 -0700 Subject: [PATCH 06/16] feat: add notes to README --- README.md | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/README.md b/README.md index 1b84b0ad..eedbc5a1 100644 --- a/README.md +++ b/README.md @@ -10,16 +10,16 @@ We find that regular job interview questions can often be misleading and so use Each file represents an assignment similar to what one would get when hired. -| Focus | ReWote | Notes | -| ---------------| --------------------------| ------------------------------ | -| Comp. Science | [Convergence Tracker](Basis-Set-Selector.md) | | -| Comp. Science | [Basis Set Selector](Convergence-Tracker.md) | | -| Data. Science | [ML Property Predict](ML-Band-Gaps.md) | | -| Front-End / UX | [Materials Designer](Materials-Designer.md) | | -| Front-End / UX | [Flowchart Designer](Flowchart-Designer.md) | | -| Back-End / Ops | [Parallel Uploader](Flowchart-Designer.md) | | -| CI/CD, DevOps | [End-to-End Tests](Flowchart-Designer.md) | | -| HPC, Cloud Inf | [Cloud HPC Bench.](Flowchart-Designer.md) | | +| Focus | ReWote | Keywords | +| ---------------| --------------------------| ------------------------------- | +| Comp. Science | [Convergence Tracker](Basis-Set-Selector.md) | Python, OOD, DFT, Planewaves | +| Comp. Science | [Basis Set Selector](Convergence-Tracker.md) | Python, OOD, DFT, Local-orbital | +| Data. Science | [ML Property Predict](ML-Band-Gaps.md) | Python, ML Models, Scikit, Featurization | +| Front-End / UX | [Materials Designer](Materials-Designer.md) | ReactJS / UX Design, ThreeJS | +| Front-End / UX | [Flowchart Designer](Flowchart-Designer.md) | ReactJS / UX Design, DAG | +| Back-End / Ops | [Parallel Uploader](Parallel-File-Uploader.md) | Python, OOD, Threading, Objectstore | +| CI/CD, DevOps | [End-to-End Tests](End-To-End-Tests.md) | BDD tests, CI/CD workflows, Cypress | +| HPC, Cloud Inf | [Cloud HPC Bench.](Cloud-Infrastructure.md) | HPC Cluster, Linpack, Benchmarks | ## Usage From 369a81d23990b83fef6305cb510d9e5902ab1dda Mon Sep 17 00:00:00 2001 From: Timur Bazhirov Date: Fri, 1 Apr 2022 15:32:41 -0700 Subject: [PATCH 07/16] fix: github workflow -> action --- Cloud-Infrastructure.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Cloud-Infrastructure.md b/Cloud-Infrastructure.md index 1a8aad0c..2435dd1d 100644 --- a/Cloud-Infrastructure.md +++ b/Cloud-Infrastructure.md @@ -8,7 +8,7 @@ The aim of this task is to create a CI/CD pipeline (github workflow) that includ # Requirements -1. A working CI/CD pipeline - e.g. GitHub workflow - able to deploy and configure an HPC cluster +1. A working CI/CD pipeline - e.g. GitHub action - able to deploy and configure an HPC cluster 2. An automated workflow (using a configurable Github action) to benchmark one or more HPC application on one or more cloud instance type # Expectations From 257f1b5cefac603469be882986c87aaedaeaebd8 Mon Sep 17 00:00:00 2001 From: Timur Bazhirov Date: Mon, 11 Apr 2022 16:47:28 -0700 Subject: [PATCH 08/16] fix: typo --- Cloud-Infrastructure.md | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/Cloud-Infrastructure.md b/Cloud-Infrastructure.md index 2435dd1d..9397d7b9 100644 --- a/Cloud-Infrastructure.md +++ b/Cloud-Infrastructure.md @@ -13,8 +13,7 @@ The aim of this task is to create a CI/CD pipeline (github workflow) that includ # Expectations -- The application may be relatively simple - e.g. Linpack, this is focused more on application infrastructure and DevOps, but the tests must actually verify functionality -- Correctly passes the tests in automation and displays coverage metrics +- The application may be relatively simple - e.g. Linpack, this is focused more on infrastructure - Clean workflow logic # Timeline @@ -23,7 +22,7 @@ We leave exact timing to the candidate. Should fit Within 5 days total. # User story -As a user of this CI/CD pipelin I can: +As a user of this CI/CD pipeline I can: - initiate tests for a specific number of scenarios: e.g. 2 nodes, 16 core per node - select the instance type to be used From 65b312ddceb3b75e2d23b3cc26e1df3795199364 Mon Sep 17 00:00:00 2001 From: Timur Bazhirov Date: Mon, 11 Apr 2022 16:47:51 -0700 Subject: [PATCH 09/16] feat: add containerization/HPC rewote --- Containerization-HPC.md | 44 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 Containerization-HPC.md diff --git a/Containerization-HPC.md b/Containerization-HPC.md new file mode 100644 index 00000000..0c9698ad --- /dev/null +++ b/Containerization-HPC.md @@ -0,0 +1,44 @@ +# Containerization / Benchmarks (HPC) + +> Ideal candidate: skilled HPC engineer versed in HPC, and Containers + +# Overview + +The aim of this task is to build an HPC compatible container (i.e. [Singularity](https://sylabs.io/guides/3.5/user-guide/introduction.html)) and test its performance in comparison with a native installation (no containerization) for a set of distributed memory calculations. + +# Requirements + +1. A working deployment pipeline - using any preferred tool such as SaltStack, Terraform, CloudFormation - for building out the computational infrastructure +2. A pipeline for building the HPC compatible container +3. A set of benchmarks for one or more HPC application on one or more cloud instance type + +# Expectations + +- The application may be relatively simple - e.g. Linpack, this is focused more on infrastructure +- Repeatable approach (no manual setup "in console") +- Clean workflow logic + +# Timeline + +We leave exact timing to the candidate. Should fit Within 5 days total. + +# User story + +As a user of this pipeline I can: + +- build an HPC-compatible container for an HPC executable/code +- run test calculations to assert working state of this container +- (optional) compare the behavior of this container with a OS native installation + +# Notes + +- Commit early and often + +# Suggestions + +We suggest: + +- using AWS as the cloud provider +- using Exabench as the source of benchmarks: https://github.com/Exabyte-io/exabyte-benchmarks-suite +- using CentOS or similar as operating system +- using Terraform for infrastructure management From 09f975caa7fe9facc219617a67a93f8e9b30b4ac Mon Sep 17 00:00:00 2001 From: Timur Bazhirov Date: Mon, 11 Apr 2022 16:50:59 -0700 Subject: [PATCH 10/16] feat: update README --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index eedbc5a1..40982842 100644 --- a/README.md +++ b/README.md @@ -20,6 +20,7 @@ Each file represents an assignment similar to what one would get when hired. | Back-End / Ops | [Parallel Uploader](Parallel-File-Uploader.md) | Python, OOD, Threading, Objectstore | | CI/CD, DevOps | [End-to-End Tests](End-To-End-Tests.md) | BDD tests, CI/CD workflows, Cypress | | HPC, Cloud Inf | [Cloud HPC Bench.](Cloud-Infrastructure.md) | HPC Cluster, Linpack, Benchmarks | +| HPC, Containers| [Conteinerized HPC](Conteinerization-HPC.md) | HPC Cluster, Containers, Benchmarks | ## Usage From b930341cf776d54adc3ef83184cbc81725e596fe Mon Sep 17 00:00:00 2001 From: Timur Bazhirov Date: Mon, 11 Apr 2022 16:59:06 -0700 Subject: [PATCH 11/16] feat: recommend usign Salt, then Terraform --- Containerization-HPC.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Containerization-HPC.md b/Containerization-HPC.md index 0c9698ad..bf3cb8db 100644 --- a/Containerization-HPC.md +++ b/Containerization-HPC.md @@ -41,4 +41,4 @@ We suggest: - using AWS as the cloud provider - using Exabench as the source of benchmarks: https://github.com/Exabyte-io/exabyte-benchmarks-suite - using CentOS or similar as operating system -- using Terraform for infrastructure management +- using Salstack, or Terraform, for infrastructure management From 3d1f87566a5ff86af7320770f2abfe8b55cc035a Mon Sep 17 00:00:00 2001 From: Timur Bazhirov Date: Mon, 11 Apr 2022 17:23:38 -0700 Subject: [PATCH 12/16] fix: typo --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 40982842..3463b969 100644 --- a/README.md +++ b/README.md @@ -20,7 +20,7 @@ Each file represents an assignment similar to what one would get when hired. | Back-End / Ops | [Parallel Uploader](Parallel-File-Uploader.md) | Python, OOD, Threading, Objectstore | | CI/CD, DevOps | [End-to-End Tests](End-To-End-Tests.md) | BDD tests, CI/CD workflows, Cypress | | HPC, Cloud Inf | [Cloud HPC Bench.](Cloud-Infrastructure.md) | HPC Cluster, Linpack, Benchmarks | -| HPC, Containers| [Conteinerized HPC](Conteinerization-HPC.md) | HPC Cluster, Containers, Benchmarks | +| HPC, Containers| [Containerized HPC](Containerization-HPC.md) | HPC Cluster, Containers, Benchmarks | ## Usage From 910655f6f5edc0688b5b4ffa2319cf8b2bbaab15 Mon Sep 17 00:00:00 2001 From: Timur Bazhirov Date: Tue, 6 Sep 2022 11:59:55 -0700 Subject: [PATCH 13/16] fix: links in README --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 3463b969..414438d3 100644 --- a/README.md +++ b/README.md @@ -12,8 +12,8 @@ Each file represents an assignment similar to what one would get when hired. | Focus | ReWote | Keywords | | ---------------| --------------------------| ------------------------------- | -| Comp. Science | [Convergence Tracker](Basis-Set-Selector.md) | Python, OOD, DFT, Planewaves | -| Comp. Science | [Basis Set Selector](Convergence-Tracker.md) | Python, OOD, DFT, Local-orbital | +| Comp. Science | [Convergence Tracker](Convergence-Tracker.md) | Python, OOD, DFT, Planewaves | +| Comp. Science | [Basis Set Selector](Basis-Set-Selector.md) | Python, OOD, DFT, Local-orbital | | Data. Science | [ML Property Predict](ML-Band-Gaps.md) | Python, ML Models, Scikit, Featurization | | Front-End / UX | [Materials Designer](Materials-Designer.md) | ReactJS / UX Design, ThreeJS | | Front-End / UX | [Flowchart Designer](Flowchart-Designer.md) | ReactJS / UX Design, DAG | From ddb871bafaa02a0fabc96bb31d305161636c743e Mon Sep 17 00:00:00 2001 From: cpolanco Date: Wed, 7 Dec 2022 00:48:07 +0100 Subject: [PATCH 14/16] Did the initial structe of the code. Create a class to handle QE input files. Create functions to read the input and create other inputs base on the class. For the moment this only works for kgrid. --- capolanco/README.md | 37 ++ capolanco/RunConvergence.py | 53 +++ capolanco/Si.scf.in | 30 ++ capolanco/Si.scf.out | 437 ++++++++++++++++++ .../__pycache__/ioqeclass.cpython-39.pyc | Bin 0 -> 1529 bytes capolanco/ioqeclass.py | 90 ++++ capolanco/test.scf.in | 30 ++ capolanco/test.scf.out | 437 ++++++++++++++++++ 8 files changed, 1114 insertions(+) create mode 100644 capolanco/README.md create mode 100644 capolanco/RunConvergence.py create mode 100644 capolanco/Si.scf.in create mode 100644 capolanco/Si.scf.out create mode 100644 capolanco/__pycache__/ioqeclass.cpython-39.pyc create mode 100644 capolanco/ioqeclass.py create mode 100644 capolanco/test.scf.in create mode 100644 capolanco/test.scf.out diff --git a/capolanco/README.md b/capolanco/README.md new file mode 100644 index 00000000..cbd01009 --- /dev/null +++ b/capolanco/README.md @@ -0,0 +1,37 @@ +# K-point convergence tracker (Materials) + +> Ideal candidate: scientists skilled in Density Functional Theory and proficient in python. + +# Overview + +The aim of this task is to create a python package that implements automatic convergence tracking mechanism for a materials simulations engine. The convergence is tracked with respect to the k-point sampling inside a reciprocal cell of a crystalline compound. + +# Requirements + +1. automatically find the dimensions of a k-point mesh that satisfy a certain criteria for total energy (eg. total energy is converged within dE = 0.01meV) +1. the code shall be written in a way that can facilitate easy addition of convergence wrt other characteristics extracted from simulations (forces, pressures, phonon frequencies etc) +1. the code shall support VASP or Quantum ESPRESSO + +# Expectations + +- correctly find k-point mesh that satisfies total energy convergence parameters for a set of 10 materials, starting from Si2, as simplest, to a 10-20-atom supercell of your choice +- modular and object-oriented implementation +- commit early and often - at least once per 24 hours + +# Timeline + +We leave exact timing to the candidate. Must fit Within 5 days total. + +# User story + +As a user of this software I can start it passing: + +- path to input data (eg. pw.in / POSCAR, INCAR, KPOINTS) and +- kinetic energy cutoff + +as parameters and get the k-point dimensions (eg. 5 5 5). + +# Notes + +- create an account at exabyte.io and use it for the calculation purposes +- suggested modeling engine: Quantum ESPRESSO diff --git a/capolanco/RunConvergence.py b/capolanco/RunConvergence.py new file mode 100644 index 00000000..f9256a09 --- /dev/null +++ b/capolanco/RunConvergence.py @@ -0,0 +1,53 @@ +# This code will run a k-point convergence up to a desire delta energy + + +import ioqeclass as qe + +########################### +##### USER INPUTS +########################### + +# Define the path of the input file +# The k-grid of this file will be set as the starting point +# for the convergence process +filein='Si.scf.in' + +# Define delta energy threshold for +# convergence (eV) +dE=1 # (eV) + + + +########################### +##### PROGRAM +########################### + + +### Set up initial parameters +# Initialize pw.x input class +qeinput=qe.qepwinput() +# load the pw.x input +qeinput.load(filein) +# Create the input file for initial run +testin='test.scf.in' +testout='test.scf.out' +qeinput.save(filein,testin) +# Run initial test +##### pw.x test.scf.in test.scf.out +# Read the Total energy from the output + + +# Loop testing for dE + +## set up calculation +#fileout='test.scf.in' +#qeinput.save(filein,fileout) + +## run pw.x + +## extract the total energy + +## compare with the threshold + + + diff --git a/capolanco/Si.scf.in b/capolanco/Si.scf.in new file mode 100644 index 00000000..0bd51ddd --- /dev/null +++ b/capolanco/Si.scf.in @@ -0,0 +1,30 @@ + &control + calculation='scf', + outdir = '/global/cscratch1/sd/cpolanco/Si/', + prefix='Si', + pseudo_dir = '/global/homes/c/cpolanco/Materials/pseudo/', + restart_mode='from_scratch', + tprnfor= .true., + tstress= .true., + / + &system + ibrav= 2, + celldm(1)= 10.20777693, + nat= 2, + ntyp= 1, + ecutwfc= 100.0 + / + &electrons + mixing_beta= 0.7 + conv_thr= 1.0d-14 + / + +ATOMIC_SPECIES + Si 28.086 Si.pz-vbc.UPF + +ATOMIC_POSITIONS (alat) + Si 0.00 0.00 0.00 + Si 0.25 0.25 0.25 + +K_POINTS (automatic) + 8 8 8 0 0 0 diff --git a/capolanco/Si.scf.out b/capolanco/Si.scf.out new file mode 100644 index 00000000..ce3f6334 --- /dev/null +++ b/capolanco/Si.scf.out @@ -0,0 +1,437 @@ + + Program PWSCF v.6.1 starts on 27Sep2017 at 19:30: 1 + + This program is part of the open-source Quantum ESPRESSO suite + for quantum simulation of materials; please cite + "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); + URL http://www.quantum-espresso.org", + in publications or presentations arising from this work. More details at + http://www.quantum-espresso.org/quote + + Parallel version (MPI & OpenMP), running on 24 processor cores + Number of MPI processes: 24 + Threads/MPI process: 1 + R & G space division: proc/nbgrp/npool/nimage = 24 + Waiting for input... + Reading input from standard input + + Current dimensions of program PWSCF are: + Max number of different atomic species (ntypx) = 10 + Max number of k-points (npk) = 40000 + Max angular momentum in pseudopotentials (lmaxx) = 3 + + Subspace diagonalization in iterative solution of the eigenvalue problem: + a serial algorithm will be used + + + Parallelization info + -------------------- + sticks: dense smooth PW G-vecs: dense smooth PW + Min 59 59 17 1489 1489 232 + Max 60 60 18 1494 1494 235 + Sum 1417 1417 421 35749 35749 5601 + + + + bravais-lattice index = 2 + lattice parameter (alat) = 10.2078 a.u. + unit-cell volume = 265.9093 (a.u.)^3 + number of atoms/cell = 2 + number of atomic types = 1 + number of electrons = 8.00 + number of Kohn-Sham states= 4 + kinetic-energy cutoff = 100.0000 Ry + charge density cutoff = 400.0000 Ry + convergence threshold = 1.0E-14 + mixing beta = 0.7000 + number of iterations used = 8 plain mixing + Exchange-correlation = SLA PZ NOGX NOGC ( 1 1 0 0 0 0) + + celldm(1)= 10.207777 celldm(2)= 0.000000 celldm(3)= 0.000000 + celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000 + + crystal axes: (cart. coord. in units of alat) + a(1) = ( -0.500000 0.000000 0.500000 ) + a(2) = ( 0.000000 0.500000 0.500000 ) + a(3) = ( -0.500000 0.500000 0.000000 ) + + reciprocal axes: (cart. coord. in units 2 pi/alat) + b(1) = ( -1.000000 -1.000000 1.000000 ) + b(2) = ( 1.000000 1.000000 1.000000 ) + b(3) = ( -1.000000 1.000000 -1.000000 ) + + + PseudoPot. # 1 for Si read from file: + /global/homes/c/cpolanco/Materials/pseudo/Si.pz-vbc.UPF + MD5 check sum: 6dfa03ddd5817404712e03e4d12deb78 + Pseudo is Norm-conserving, Zval = 4.0 + Generated by new atomic code, or converted to UPF format + Using radial grid of 431 points, 2 beta functions with: + l(1) = 0 + l(2) = 1 + + atomic species valence mass pseudopotential + Si 4.00 28.08600 Si( 1.00) + + 24 Sym. Ops. (no inversion) found + (note: 24 additional sym.ops. were found but ignored + their fractional translations are incommensurate with FFT grid) + + + Cartesian axes + + site n. atom positions (alat units) + 1 Si tau( 1) = ( 0.0000000 0.0000000 0.0000000 ) + 2 Si tau( 2) = ( 0.2500000 0.2500000 0.2500000 ) + + number of k points= 29 + cart. coord. in units 2pi/alat + k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 0.0039062 + k( 2) = ( -0.1250000 0.1250000 -0.1250000), wk = 0.0312500 + k( 3) = ( -0.2500000 0.2500000 -0.2500000), wk = 0.0312500 + k( 4) = ( -0.3750000 0.3750000 -0.3750000), wk = 0.0312500 + k( 5) = ( 0.5000000 -0.5000000 0.5000000), wk = 0.0156250 + k( 6) = ( 0.0000000 0.2500000 0.0000000), wk = 0.0234375 + k( 7) = ( -0.1250000 0.3750000 -0.1250000), wk = 0.0937500 + k( 8) = ( -0.2500000 0.5000000 -0.2500000), wk = 0.0937500 + k( 9) = ( 0.6250000 -0.3750000 0.6250000), wk = 0.0937500 + k( 10) = ( 0.5000000 -0.2500000 0.5000000), wk = 0.0937500 + k( 11) = ( 0.3750000 -0.1250000 0.3750000), wk = 0.0937500 + k( 12) = ( 0.2500000 0.0000000 0.2500000), wk = 0.0468750 + k( 13) = ( 0.0000000 0.5000000 0.0000000), wk = 0.0234375 + k( 14) = ( -0.1250000 0.6250000 -0.1250000), wk = 0.0937500 + k( 15) = ( 0.7500000 -0.2500000 0.7500000), wk = 0.0937500 + k( 16) = ( 0.6250000 -0.1250000 0.6250000), wk = 0.0937500 + k( 17) = ( 0.5000000 0.0000000 0.5000000), wk = 0.0468750 + k( 18) = ( 0.0000000 0.7500000 0.0000000), wk = 0.0234375 + k( 19) = ( 0.8750000 -0.1250000 0.8750000), wk = 0.0937500 + k( 20) = ( 0.7500000 0.0000000 0.7500000), wk = 0.0468750 + k( 21) = ( 0.0000000 -1.0000000 0.0000000), wk = 0.0117188 + k( 22) = ( -0.2500000 0.5000000 0.0000000), wk = 0.0937500 + k( 23) = ( 0.6250000 -0.3750000 0.8750000), wk = 0.1875000 + k( 24) = ( 0.5000000 -0.2500000 0.7500000), wk = 0.0937500 + k( 25) = ( 0.7500000 -0.2500000 1.0000000), wk = 0.0937500 + k( 26) = ( 0.6250000 -0.1250000 0.8750000), wk = 0.1875000 + k( 27) = ( 0.5000000 0.0000000 0.7500000), wk = 0.0937500 + k( 28) = ( -0.2500000 -1.0000000 0.0000000), wk = 0.0468750 + k( 29) = ( -0.5000000 -1.0000000 0.0000000), wk = 0.0234375 + + Dense grid: 35749 G-vectors FFT dimensions: ( 45, 45, 45) + + Estimated max dynamical RAM per process > 1.29MB + + Estimated total allocated dynamical RAM > 31.06MB + + Initial potential from superposition of free atoms + + starting charge 7.99901, renormalised to 8.00000 + Starting wfc are 8 randomized atomic wfcs + + total cpu time spent up to now is 0.4 secs + + per-process dynamical memory: 2.9 Mb + + Self-consistent Calculation + + iteration # 1 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.00E-02, avg # of iterations = 2.0 + + Threshold (ethr) on eigenvalues was too large: + Diagonalizing with lowered threshold + + Davidson diagonalization with overlap + ethr = 7.97E-04, avg # of iterations = 1.0 + + total cpu time spent up to now is 0.6 secs + + total energy = -15.84982619 Ry + Harris-Foulkes estimate = -15.87079416 Ry + estimated scf accuracy < 0.06161703 Ry + + iteration # 2 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 7.70E-04, avg # of iterations = 1.0 + + total cpu time spent up to now is 0.7 secs + + total energy = -15.85288351 Ry + Harris-Foulkes estimate = -15.85318795 Ry + estimated scf accuracy < 0.00216687 Ry + + iteration # 3 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 2.71E-05, avg # of iterations = 2.4 + + total cpu time spent up to now is 0.8 secs + + total energy = -15.85332918 Ry + Harris-Foulkes estimate = -15.85336185 Ry + estimated scf accuracy < 0.00007437 Ry + + iteration # 4 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 9.30E-07, avg # of iterations = 2.1 + + total cpu time spent up to now is 0.8 secs + + total energy = -15.85334986 Ry + Harris-Foulkes estimate = -15.85335396 Ry + estimated scf accuracy < 0.00000888 Ry + + iteration # 5 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.11E-07, avg # of iterations = 2.1 + + total cpu time spent up to now is 0.9 secs + + total energy = -15.85335134 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 0.00000011 Ry + + iteration # 6 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.35E-09, avg # of iterations = 2.6 + + total cpu time spent up to now is 1.0 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 2.9E-09 Ry + + iteration # 7 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 3.68E-11, avg # of iterations = 2.6 + + total cpu time spent up to now is 1.1 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 2.9E-11 Ry + + iteration # 8 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 3.65E-13, avg # of iterations = 3.3 + + total cpu time spent up to now is 1.2 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 5.4E-12 Ry + + iteration # 9 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.00E-13, avg # of iterations = 1.7 + + total cpu time spent up to now is 1.3 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 1.2E-13 Ry + + iteration # 10 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.00E-13, avg # of iterations = 1.0 + + total cpu time spent up to now is 1.4 secs + + End of self-consistent calculation + + k = 0.0000 0.0000 0.0000 ( 4477 PWs) bands (ev): + + -5.8300 6.2061 6.2061 6.2061 + + k =-0.1250 0.1250-0.1250 ( 4507 PWs) bands (ev): + + -5.6230 4.6051 5.9132 5.9132 + + k =-0.2500 0.2500-0.2500 ( 4510 PWs) bands (ev): + + -5.0182 2.2559 5.4373 5.4373 + + k =-0.3750 0.3750-0.3750 ( 4501 PWs) bands (ev): + + -4.1058 0.2065 5.1074 5.1074 + + k = 0.5000-0.5000 0.5000 ( 4476 PWs) bands (ev): + + -3.4453 -0.8427 4.9947 4.9947 + + k = 0.0000 0.2500 0.0000 ( 4504 PWs) bands (ev): + + -5.5533 4.8935 5.3857 5.3857 + + k =-0.1250 0.3750-0.1250 ( 4517 PWs) bands (ev): + + -5.0777 2.9801 4.8669 4.9518 + + k =-0.2500 0.5000-0.2500 ( 4508 PWs) bands (ev): + + -4.2481 0.8896 4.3532 4.5964 + + k = 0.6250-0.3750 0.6250 ( 4486 PWs) bands (ev): + + -3.3613 -0.6068 3.9003 4.6231 + + k = 0.5000-0.2500 0.5000 ( 4491 PWs) bands (ev): + + -3.6148 -0.2257 3.7125 4.9256 + + k = 0.3750-0.1250 0.3750 ( 4497 PWs) bands (ev): + + -4.5602 1.5598 3.8591 5.4251 + + k = 0.2500 0.0000 0.2500 ( 4477 PWs) bands (ev): + + -5.2819 3.5267 4.5444 5.9125 + + k = 0.0000 0.5000 0.0000 ( 4520 PWs) bands (ev): + + -4.7329 2.7148 4.2862 4.2862 + + k =-0.1250 0.6250-0.1250 ( 4509 PWs) bands (ev): + + -4.0117 1.2745 3.4881 3.9636 + + k = 0.7500-0.2500 0.7500 ( 4482 PWs) bands (ev): + + -3.0647 -0.1975 2.6082 3.9678 + + k = 0.6250-0.1250 0.6250 ( 4477 PWs) bands (ev): + + -2.8512 -0.4657 2.1376 4.2926 + + k = 0.5000 0.0000 0.5000 ( 4489 PWs) bands (ev): + + -3.7521 0.7207 2.3750 4.8614 + + k = 0.0000 0.7500 0.0000 ( 4484 PWs) bands (ev): + + -3.4015 0.4708 3.5586 3.5586 + + k = 0.8750-0.1250 0.8750 ( 4479 PWs) bands (ev): + + -2.4888 -0.6253 2.7002 3.4815 + + k = 0.7500 0.0000 0.7500 ( 4454 PWs) bands (ev): + + -2.0305 -1.0339 1.8049 3.7440 + + k = 0.0000-1.0000 0.0000 ( 4456 PWs) bands (ev): + + -1.6267 -1.6267 3.3090 3.3090 + + k =-0.2500 0.5000 0.0000 ( 4503 PWs) bands (ev): + + -4.4807 1.9234 3.4393 4.7592 + + k = 0.6250-0.3750 0.8750 ( 4489 PWs) bands (ev): + + -3.5748 0.3447 2.8290 4.2439 + + k = 0.5000-0.2500 0.7500 ( 4486 PWs) bands (ev): + + -2.9014 -0.6278 2.7039 4.0076 + + k = 0.7500-0.2500 1.0000 ( 4484 PWs) bands (ev): + + -3.1970 0.2501 2.7770 3.3923 + + k = 0.6250-0.1250 0.8750 ( 4486 PWs) bands (ev): + + -2.3006 -0.7332 2.0576 3.1860 + + k = 0.5000 0.0000 0.7500 ( 4490 PWs) bands (ev): + + -2.6570 -0.3670 1.8851 3.5717 + + k =-0.2500-1.0000 0.0000 ( 4472 PWs) bands (ev): + + -1.5427 -1.5427 2.7194 2.7194 + + k =-0.5000-1.0000 0.0000 ( 4488 PWs) bands (ev): + + -1.4495 -1.4495 2.2655 2.2655 + + highest occupied level (ev): 6.2061 + +! total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 4.0E-15 Ry + + The total energy is the sum of the following terms: + + one-electron contribution = 4.76680131 Ry + hartree contribution = 1.08149972 Ry + xc contribution = -4.81476914 Ry + ewald contribution = -16.88688327 Ry + + convergence has been achieved in 10 iterations + + Forces acting on atoms (cartesian axes, Ry/au): + + atom 1 type 1 force = 0.00000000 0.00000000 0.00000000 + atom 2 type 1 force = 0.00000000 0.00000000 -0.00000000 + + Total force = 0.000000 Total SCF correction = 0.000000 + + + Computing stress (Cartesian axis) and pressure + + total stress (Ry/bohr**3) (kbar) P= 0.05 + 0.00000032 -0.00000000 -0.00000000 0.05 -0.00 -0.00 + -0.00000000 0.00000032 0.00000000 -0.00 0.05 0.00 + -0.00000000 0.00000000 0.00000032 -0.00 0.00 0.05 + + + Writing output data file Si.save + + init_run : 0.06s CPU 0.23s WALL ( 1 calls) + electrons : 0.85s CPU 1.01s WALL ( 1 calls) + forces : 0.00s CPU 0.01s WALL ( 1 calls) + stress : 0.02s CPU 0.03s WALL ( 1 calls) + + Called by init_run: + wfcinit : 0.04s CPU 0.11s WALL ( 1 calls) + potinit : 0.00s CPU 0.01s WALL ( 1 calls) + + Called by electrons: + c_bands : 0.73s CPU 0.80s WALL ( 11 calls) + sum_band : 0.11s CPU 0.13s WALL ( 11 calls) + v_of_rho : 0.00s CPU 0.01s WALL ( 11 calls) + mix_rho : 0.00s CPU 0.01s WALL ( 11 calls) + + Called by c_bands: + init_us_2 : 0.01s CPU 0.03s WALL ( 725 calls) + cegterg : 0.69s CPU 0.74s WALL ( 319 calls) + + Called by sum_band: + + Called by *egterg: + h_psi : 0.62s CPU 0.65s WALL ( 980 calls) + g_psi : 0.00s CPU 0.00s WALL ( 632 calls) + cdiaghg : 0.05s CPU 0.10s WALL ( 922 calls) + + Called by h_psi: + h_psi:pot : 0.61s CPU 0.65s WALL ( 980 calls) + h_psi:calbec : 0.03s CPU 0.04s WALL ( 980 calls) + vloc_psi : 0.57s CPU 0.59s WALL ( 980 calls) + add_vuspsi : 0.01s CPU 0.01s WALL ( 980 calls) + + General routines + calbec : 0.03s CPU 0.05s WALL ( 1125 calls) + fft : 0.01s CPU 0.05s WALL ( 50 calls) + fftw : 0.57s CPU 0.64s WALL ( 8656 calls) + davcio : 0.00s CPU 0.06s WALL ( 29 calls) + + Parallel routines + fft_scatter : 0.29s CPU 0.31s WALL ( 8706 calls) + + PWSCF : 1.07s CPU 2.22s WALL + + + This run was terminated on: 19:30: 3 27Sep2017 + +=------------------------------------------------------------------------------= + JOB DONE. +=------------------------------------------------------------------------------= diff --git a/capolanco/__pycache__/ioqeclass.cpython-39.pyc b/capolanco/__pycache__/ioqeclass.cpython-39.pyc new file mode 100644 index 0000000000000000000000000000000000000000..6c31709eab9824c949939c8e250b7c00b26c1d2e GIT binary patch literal 1529 zcmZ{kPjB2r6u@W3p0%@00#xNs5TFscU=*^IfQUnciYOrdXbVcYtb{DbGfCZgZSNaz zw^=!-^osZZRi%Uj5}$|LTsh?{*1VZ{Z{E|J`Mq(nvC(JPKK<*r^rJP# z{-(uh^KfwoyL}slW}4@0#J^!$XzwZ0-kBH)%@0`QU!t82QW%`4l&xATbr0_mKD{so_~G+L1tB&C)O%$Yzo<-v8sMx)KAl- zsHbD~m94;7TdLMU9hIOGRn2yvs5HsbX`a+sS)?2@xNbD}v44r(zJ;P@5BV`3?{`j# z{VEz33(e?Y!^pd&?Lb%23MaFo-uootn00+pnaFdZs75jYNKTx5bPSn}xbv;akN#v3 zqTkiM!Ozx!9i&NB=1Gy3gS%xq9h;)IgYU}2FRCif(l*b*IH^B|WB_JX)@IcsD<`JC zhTZDKg>jq}Sslmg7~aw~GjD!#d274Z=Cn1D8JonuJoX>BsPV{WoYN>4qu20f?0L81 z4cGpeI2Db!%YIR(UgMpM3wG)^KI}9|Zj0&OBLO>{O@@=5Mx1+SUGA#=bJ^{>;0=4& z({i6Jbio!|=z^s#TGP^|9J1);r)Y_uRWNaKiaz5>M{7K8a6ZohY>M^-DaAw~_!TgYieADaGD15%odxA8#=o9nJ ze<6}vN_BVLC;^Jt*6m9HiWdO#nm0mAM2UD2<%ft6Q8xYs!f*T*n`|WPHTVz_YJgDp z5bEJ%kM`*h@%dzV#`Ib{@2|{nwDa}nK^x6Gmjtfi-Pi)$7{U!q8>m?4?;@>(UEVz-gmDl2jtMgcucDu+0B{Wu<% zdYaRGJ&q^SBwtv9IM!tv$3Q<{*djrNv62Y=G=NA0l_;IZk}BlB4Ey2xtv2#TvY3vm YldeK( 1.29MB + + Estimated total allocated dynamical RAM > 31.06MB + + Initial potential from superposition of free atoms + + starting charge 7.99901, renormalised to 8.00000 + Starting wfc are 8 randomized atomic wfcs + + total cpu time spent up to now is 0.4 secs + + per-process dynamical memory: 2.9 Mb + + Self-consistent Calculation + + iteration # 1 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.00E-02, avg # of iterations = 2.0 + + Threshold (ethr) on eigenvalues was too large: + Diagonalizing with lowered threshold + + Davidson diagonalization with overlap + ethr = 7.97E-04, avg # of iterations = 1.0 + + total cpu time spent up to now is 0.6 secs + + total energy = -15.84982619 Ry + Harris-Foulkes estimate = -15.87079416 Ry + estimated scf accuracy < 0.06161703 Ry + + iteration # 2 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 7.70E-04, avg # of iterations = 1.0 + + total cpu time spent up to now is 0.7 secs + + total energy = -15.85288351 Ry + Harris-Foulkes estimate = -15.85318795 Ry + estimated scf accuracy < 0.00216687 Ry + + iteration # 3 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 2.71E-05, avg # of iterations = 2.4 + + total cpu time spent up to now is 0.8 secs + + total energy = -15.85332918 Ry + Harris-Foulkes estimate = -15.85336185 Ry + estimated scf accuracy < 0.00007437 Ry + + iteration # 4 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 9.30E-07, avg # of iterations = 2.1 + + total cpu time spent up to now is 0.8 secs + + total energy = -15.85334986 Ry + Harris-Foulkes estimate = -15.85335396 Ry + estimated scf accuracy < 0.00000888 Ry + + iteration # 5 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.11E-07, avg # of iterations = 2.1 + + total cpu time spent up to now is 0.9 secs + + total energy = -15.85335134 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 0.00000011 Ry + + iteration # 6 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.35E-09, avg # of iterations = 2.6 + + total cpu time spent up to now is 1.0 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 2.9E-09 Ry + + iteration # 7 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 3.68E-11, avg # of iterations = 2.6 + + total cpu time spent up to now is 1.1 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 2.9E-11 Ry + + iteration # 8 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 3.65E-13, avg # of iterations = 3.3 + + total cpu time spent up to now is 1.2 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 5.4E-12 Ry + + iteration # 9 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.00E-13, avg # of iterations = 1.7 + + total cpu time spent up to now is 1.3 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 1.2E-13 Ry + + iteration # 10 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.00E-13, avg # of iterations = 1.0 + + total cpu time spent up to now is 1.4 secs + + End of self-consistent calculation + + k = 0.0000 0.0000 0.0000 ( 4477 PWs) bands (ev): + + -5.8300 6.2061 6.2061 6.2061 + + k =-0.1250 0.1250-0.1250 ( 4507 PWs) bands (ev): + + -5.6230 4.6051 5.9132 5.9132 + + k =-0.2500 0.2500-0.2500 ( 4510 PWs) bands (ev): + + -5.0182 2.2559 5.4373 5.4373 + + k =-0.3750 0.3750-0.3750 ( 4501 PWs) bands (ev): + + -4.1058 0.2065 5.1074 5.1074 + + k = 0.5000-0.5000 0.5000 ( 4476 PWs) bands (ev): + + -3.4453 -0.8427 4.9947 4.9947 + + k = 0.0000 0.2500 0.0000 ( 4504 PWs) bands (ev): + + -5.5533 4.8935 5.3857 5.3857 + + k =-0.1250 0.3750-0.1250 ( 4517 PWs) bands (ev): + + -5.0777 2.9801 4.8669 4.9518 + + k =-0.2500 0.5000-0.2500 ( 4508 PWs) bands (ev): + + -4.2481 0.8896 4.3532 4.5964 + + k = 0.6250-0.3750 0.6250 ( 4486 PWs) bands (ev): + + -3.3613 -0.6068 3.9003 4.6231 + + k = 0.5000-0.2500 0.5000 ( 4491 PWs) bands (ev): + + -3.6148 -0.2257 3.7125 4.9256 + + k = 0.3750-0.1250 0.3750 ( 4497 PWs) bands (ev): + + -4.5602 1.5598 3.8591 5.4251 + + k = 0.2500 0.0000 0.2500 ( 4477 PWs) bands (ev): + + -5.2819 3.5267 4.5444 5.9125 + + k = 0.0000 0.5000 0.0000 ( 4520 PWs) bands (ev): + + -4.7329 2.7148 4.2862 4.2862 + + k =-0.1250 0.6250-0.1250 ( 4509 PWs) bands (ev): + + -4.0117 1.2745 3.4881 3.9636 + + k = 0.7500-0.2500 0.7500 ( 4482 PWs) bands (ev): + + -3.0647 -0.1975 2.6082 3.9678 + + k = 0.6250-0.1250 0.6250 ( 4477 PWs) bands (ev): + + -2.8512 -0.4657 2.1376 4.2926 + + k = 0.5000 0.0000 0.5000 ( 4489 PWs) bands (ev): + + -3.7521 0.7207 2.3750 4.8614 + + k = 0.0000 0.7500 0.0000 ( 4484 PWs) bands (ev): + + -3.4015 0.4708 3.5586 3.5586 + + k = 0.8750-0.1250 0.8750 ( 4479 PWs) bands (ev): + + -2.4888 -0.6253 2.7002 3.4815 + + k = 0.7500 0.0000 0.7500 ( 4454 PWs) bands (ev): + + -2.0305 -1.0339 1.8049 3.7440 + + k = 0.0000-1.0000 0.0000 ( 4456 PWs) bands (ev): + + -1.6267 -1.6267 3.3090 3.3090 + + k =-0.2500 0.5000 0.0000 ( 4503 PWs) bands (ev): + + -4.4807 1.9234 3.4393 4.7592 + + k = 0.6250-0.3750 0.8750 ( 4489 PWs) bands (ev): + + -3.5748 0.3447 2.8290 4.2439 + + k = 0.5000-0.2500 0.7500 ( 4486 PWs) bands (ev): + + -2.9014 -0.6278 2.7039 4.0076 + + k = 0.7500-0.2500 1.0000 ( 4484 PWs) bands (ev): + + -3.1970 0.2501 2.7770 3.3923 + + k = 0.6250-0.1250 0.8750 ( 4486 PWs) bands (ev): + + -2.3006 -0.7332 2.0576 3.1860 + + k = 0.5000 0.0000 0.7500 ( 4490 PWs) bands (ev): + + -2.6570 -0.3670 1.8851 3.5717 + + k =-0.2500-1.0000 0.0000 ( 4472 PWs) bands (ev): + + -1.5427 -1.5427 2.7194 2.7194 + + k =-0.5000-1.0000 0.0000 ( 4488 PWs) bands (ev): + + -1.4495 -1.4495 2.2655 2.2655 + + highest occupied level (ev): 6.2061 + +! total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 4.0E-15 Ry + + The total energy is the sum of the following terms: + + one-electron contribution = 4.76680131 Ry + hartree contribution = 1.08149972 Ry + xc contribution = -4.81476914 Ry + ewald contribution = -16.88688327 Ry + + convergence has been achieved in 10 iterations + + Forces acting on atoms (cartesian axes, Ry/au): + + atom 1 type 1 force = 0.00000000 0.00000000 0.00000000 + atom 2 type 1 force = 0.00000000 0.00000000 -0.00000000 + + Total force = 0.000000 Total SCF correction = 0.000000 + + + Computing stress (Cartesian axis) and pressure + + total stress (Ry/bohr**3) (kbar) P= 0.05 + 0.00000032 -0.00000000 -0.00000000 0.05 -0.00 -0.00 + -0.00000000 0.00000032 0.00000000 -0.00 0.05 0.00 + -0.00000000 0.00000000 0.00000032 -0.00 0.00 0.05 + + + Writing output data file Si.save + + init_run : 0.06s CPU 0.23s WALL ( 1 calls) + electrons : 0.85s CPU 1.01s WALL ( 1 calls) + forces : 0.00s CPU 0.01s WALL ( 1 calls) + stress : 0.02s CPU 0.03s WALL ( 1 calls) + + Called by init_run: + wfcinit : 0.04s CPU 0.11s WALL ( 1 calls) + potinit : 0.00s CPU 0.01s WALL ( 1 calls) + + Called by electrons: + c_bands : 0.73s CPU 0.80s WALL ( 11 calls) + sum_band : 0.11s CPU 0.13s WALL ( 11 calls) + v_of_rho : 0.00s CPU 0.01s WALL ( 11 calls) + mix_rho : 0.00s CPU 0.01s WALL ( 11 calls) + + Called by c_bands: + init_us_2 : 0.01s CPU 0.03s WALL ( 725 calls) + cegterg : 0.69s CPU 0.74s WALL ( 319 calls) + + Called by sum_band: + + Called by *egterg: + h_psi : 0.62s CPU 0.65s WALL ( 980 calls) + g_psi : 0.00s CPU 0.00s WALL ( 632 calls) + cdiaghg : 0.05s CPU 0.10s WALL ( 922 calls) + + Called by h_psi: + h_psi:pot : 0.61s CPU 0.65s WALL ( 980 calls) + h_psi:calbec : 0.03s CPU 0.04s WALL ( 980 calls) + vloc_psi : 0.57s CPU 0.59s WALL ( 980 calls) + add_vuspsi : 0.01s CPU 0.01s WALL ( 980 calls) + + General routines + calbec : 0.03s CPU 0.05s WALL ( 1125 calls) + fft : 0.01s CPU 0.05s WALL ( 50 calls) + fftw : 0.57s CPU 0.64s WALL ( 8656 calls) + davcio : 0.00s CPU 0.06s WALL ( 29 calls) + + Parallel routines + fft_scatter : 0.29s CPU 0.31s WALL ( 8706 calls) + + PWSCF : 1.07s CPU 2.22s WALL + + + This run was terminated on: 19:30: 3 27Sep2017 + +=------------------------------------------------------------------------------= + JOB DONE. +=------------------------------------------------------------------------------= From 4932df23a15f043acec160e9f6eb34d4ae25f8a7 Mon Sep 17 00:00:00 2001 From: cpolanco Date: Wed, 7 Dec 2022 23:47:09 +0100 Subject: [PATCH 15/16] The core convergence program is working. The code iterates on fictituos files until achieving convergence. This program should work in principle for any valid input given in QE --- capolanco/RunConvergence.py | 59 ++- .../__pycache__/ioqeclass.cpython-39.pyc | Bin 1529 -> 2292 bytes capolanco/ioqeclass.py | 42 ++ capolanco/test.scf1.in | 30 ++ capolanco/test.scf1.out | 437 ++++++++++++++++++ capolanco/test.scf2.in | 30 ++ capolanco/test.scf2.out | 437 ++++++++++++++++++ capolanco/test.scf3.in | 30 ++ capolanco/test.scf3.out | 437 ++++++++++++++++++ capolanco/test.scf4.in | 30 ++ capolanco/test.scf4.out | 437 ++++++++++++++++++ 11 files changed, 1957 insertions(+), 12 deletions(-) create mode 100644 capolanco/test.scf1.in create mode 100644 capolanco/test.scf1.out create mode 100644 capolanco/test.scf2.in create mode 100644 capolanco/test.scf2.out create mode 100644 capolanco/test.scf3.in create mode 100644 capolanco/test.scf3.out create mode 100644 capolanco/test.scf4.in create mode 100644 capolanco/test.scf4.out diff --git a/capolanco/RunConvergence.py b/capolanco/RunConvergence.py index f9256a09..b78b0abd 100644 --- a/capolanco/RunConvergence.py +++ b/capolanco/RunConvergence.py @@ -14,9 +14,17 @@ # Define delta energy threshold for # convergence (eV) -dE=1 # (eV) +dEthreshold=1.0 # (eV) +########################### +##### DEVELOPERS INPUTS +########################### + +# maximum of iterations +Nitermax=20 +# increasing step of kgrid +kstep=2 ########################### ##### PROGRAM @@ -34,20 +42,47 @@ qeinput.save(filein,testin) # Run initial test ##### pw.x test.scf.in test.scf.out +# Initialize pw.x output class +qeoutput=qe.qepwoutput() # Read the Total energy from the output +qeoutput.getenergy(testout) # Loop testing for dE - -## set up calculation -#fileout='test.scf.in' -#qeinput.save(filein,fileout) - -## run pw.x - -## extract the total energy - -## compare with the threshold - +dE=2.0*dEthreshold +EnergyOld=qeoutput.energy +counter=0 +while ((dE>dEthreshold) and (counterG(#D!j9#ujQT*4odz-^|X;&dmPK{hG@=Gc#EN<4-ZF z74lJjk*-9mrQ$;(48h(L!QN>*x}eX9ZAOoN+7r6NMA-MGt;br+kC~&C(~sG{s~TcL zV?u4k^k)&T}$pp*FK(GK}R`c3{oG_IgZ|UV+4h0EJAJue=nt3G7jXOqVG>iJQ zrzlc$00WKlW6G6|#Car4zJZ@@sseIFfSC1EBa~_$33RD00)PhIF}6b4^gRdUB@~qr zE+H%;oQj5!ae+0j%pkplaP_Q08uR!gyBs|(Qy%RvZ$g4HakeA*`mlJKXtRa#fDHMmu&@Tbxdjh4&9cIbFKjhpYPc9Z+P^|zQ1$X`nAHXv;Zdm(9r zW4ipq7{Si{{`FIR>CWn1J9AR}wCYJpR`7(4fb~}k2xsa`;we{#sqcM|2B<UMO p$|js`?66k1>G#v3Vl@)}KO@+-v9;N3i>@cP@O=dM!Yr15@fQd7%H99~ delta 371 zcmZvYKTg9i6o=zDFLenC6!9+=DnU#ZLSkX7H~||A$`&;SRU~bANmZpwkAR|_f`O?Q z;0|m)24aB;zp{XYEq%lH`^kRxNAJ@M65rpj%({Gg8l88W;E45`v(Qc1jU}Dt_FYOA zLt52^l3d%9B8CJpsWm*@<2aQ}JEh9*o-GuslD)DJ%vtCVTmucGY+5P_*lDkM-xCz9 z(Oo@q!Ca5TX1jDwmp=8`92u#=U|~nm7mJXS*dpOZ7qq2|+vIu%8s<2z6z-6qD{ 1.29MB + + Estimated total allocated dynamical RAM > 31.06MB + + Initial potential from superposition of free atoms + + starting charge 7.99901, renormalised to 8.00000 + Starting wfc are 8 randomized atomic wfcs + + total cpu time spent up to now is 0.4 secs + + per-process dynamical memory: 2.9 Mb + + Self-consistent Calculation + + iteration # 1 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.00E-02, avg # of iterations = 2.0 + + Threshold (ethr) on eigenvalues was too large: + Diagonalizing with lowered threshold + + Davidson diagonalization with overlap + ethr = 7.97E-04, avg # of iterations = 1.0 + + total cpu time spent up to now is 0.6 secs + + total energy = -15.84982619 Ry + Harris-Foulkes estimate = -15.87079416 Ry + estimated scf accuracy < 0.06161703 Ry + + iteration # 2 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 7.70E-04, avg # of iterations = 1.0 + + total cpu time spent up to now is 0.7 secs + + total energy = -15.85288351 Ry + Harris-Foulkes estimate = -15.85318795 Ry + estimated scf accuracy < 0.00216687 Ry + + iteration # 3 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 2.71E-05, avg # of iterations = 2.4 + + total cpu time spent up to now is 0.8 secs + + total energy = -15.85332918 Ry + Harris-Foulkes estimate = -15.85336185 Ry + estimated scf accuracy < 0.00007437 Ry + + iteration # 4 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 9.30E-07, avg # of iterations = 2.1 + + total cpu time spent up to now is 0.8 secs + + total energy = -15.85334986 Ry + Harris-Foulkes estimate = -15.85335396 Ry + estimated scf accuracy < 0.00000888 Ry + + iteration # 5 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.11E-07, avg # of iterations = 2.1 + + total cpu time spent up to now is 0.9 secs + + total energy = -15.85335134 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 0.00000011 Ry + + iteration # 6 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.35E-09, avg # of iterations = 2.6 + + total cpu time spent up to now is 1.0 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 2.9E-09 Ry + + iteration # 7 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 3.68E-11, avg # of iterations = 2.6 + + total cpu time spent up to now is 1.1 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 2.9E-11 Ry + + iteration # 8 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 3.65E-13, avg # of iterations = 3.3 + + total cpu time spent up to now is 1.2 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 5.4E-12 Ry + + iteration # 9 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.00E-13, avg # of iterations = 1.7 + + total cpu time spent up to now is 1.3 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 1.2E-13 Ry + + iteration # 10 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.00E-13, avg # of iterations = 1.0 + + total cpu time spent up to now is 1.4 secs + + End of self-consistent calculation + + k = 0.0000 0.0000 0.0000 ( 4477 PWs) bands (ev): + + -5.8300 6.2061 6.2061 6.2061 + + k =-0.1250 0.1250-0.1250 ( 4507 PWs) bands (ev): + + -5.6230 4.6051 5.9132 5.9132 + + k =-0.2500 0.2500-0.2500 ( 4510 PWs) bands (ev): + + -5.0182 2.2559 5.4373 5.4373 + + k =-0.3750 0.3750-0.3750 ( 4501 PWs) bands (ev): + + -4.1058 0.2065 5.1074 5.1074 + + k = 0.5000-0.5000 0.5000 ( 4476 PWs) bands (ev): + + -3.4453 -0.8427 4.9947 4.9947 + + k = 0.0000 0.2500 0.0000 ( 4504 PWs) bands (ev): + + -5.5533 4.8935 5.3857 5.3857 + + k =-0.1250 0.3750-0.1250 ( 4517 PWs) bands (ev): + + -5.0777 2.9801 4.8669 4.9518 + + k =-0.2500 0.5000-0.2500 ( 4508 PWs) bands (ev): + + -4.2481 0.8896 4.3532 4.5964 + + k = 0.6250-0.3750 0.6250 ( 4486 PWs) bands (ev): + + -3.3613 -0.6068 3.9003 4.6231 + + k = 0.5000-0.2500 0.5000 ( 4491 PWs) bands (ev): + + -3.6148 -0.2257 3.7125 4.9256 + + k = 0.3750-0.1250 0.3750 ( 4497 PWs) bands (ev): + + -4.5602 1.5598 3.8591 5.4251 + + k = 0.2500 0.0000 0.2500 ( 4477 PWs) bands (ev): + + -5.2819 3.5267 4.5444 5.9125 + + k = 0.0000 0.5000 0.0000 ( 4520 PWs) bands (ev): + + -4.7329 2.7148 4.2862 4.2862 + + k =-0.1250 0.6250-0.1250 ( 4509 PWs) bands (ev): + + -4.0117 1.2745 3.4881 3.9636 + + k = 0.7500-0.2500 0.7500 ( 4482 PWs) bands (ev): + + -3.0647 -0.1975 2.6082 3.9678 + + k = 0.6250-0.1250 0.6250 ( 4477 PWs) bands (ev): + + -2.8512 -0.4657 2.1376 4.2926 + + k = 0.5000 0.0000 0.5000 ( 4489 PWs) bands (ev): + + -3.7521 0.7207 2.3750 4.8614 + + k = 0.0000 0.7500 0.0000 ( 4484 PWs) bands (ev): + + -3.4015 0.4708 3.5586 3.5586 + + k = 0.8750-0.1250 0.8750 ( 4479 PWs) bands (ev): + + -2.4888 -0.6253 2.7002 3.4815 + + k = 0.7500 0.0000 0.7500 ( 4454 PWs) bands (ev): + + -2.0305 -1.0339 1.8049 3.7440 + + k = 0.0000-1.0000 0.0000 ( 4456 PWs) bands (ev): + + -1.6267 -1.6267 3.3090 3.3090 + + k =-0.2500 0.5000 0.0000 ( 4503 PWs) bands (ev): + + -4.4807 1.9234 3.4393 4.7592 + + k = 0.6250-0.3750 0.8750 ( 4489 PWs) bands (ev): + + -3.5748 0.3447 2.8290 4.2439 + + k = 0.5000-0.2500 0.7500 ( 4486 PWs) bands (ev): + + -2.9014 -0.6278 2.7039 4.0076 + + k = 0.7500-0.2500 1.0000 ( 4484 PWs) bands (ev): + + -3.1970 0.2501 2.7770 3.3923 + + k = 0.6250-0.1250 0.8750 ( 4486 PWs) bands (ev): + + -2.3006 -0.7332 2.0576 3.1860 + + k = 0.5000 0.0000 0.7500 ( 4490 PWs) bands (ev): + + -2.6570 -0.3670 1.8851 3.5717 + + k =-0.2500-1.0000 0.0000 ( 4472 PWs) bands (ev): + + -1.5427 -1.5427 2.7194 2.7194 + + k =-0.5000-1.0000 0.0000 ( 4488 PWs) bands (ev): + + -1.4495 -1.4495 2.2655 2.2655 + + highest occupied level (ev): 6.2061 + +! total energy = -16.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 4.0E-15 Ry + + The total energy is the sum of the following terms: + + one-electron contribution = 4.76680131 Ry + hartree contribution = 1.08149972 Ry + xc contribution = -4.81476914 Ry + ewald contribution = -16.88688327 Ry + + convergence has been achieved in 10 iterations + + Forces acting on atoms (cartesian axes, Ry/au): + + atom 1 type 1 force = 0.00000000 0.00000000 0.00000000 + atom 2 type 1 force = 0.00000000 0.00000000 -0.00000000 + + Total force = 0.000000 Total SCF correction = 0.000000 + + + Computing stress (Cartesian axis) and pressure + + total stress (Ry/bohr**3) (kbar) P= 0.05 + 0.00000032 -0.00000000 -0.00000000 0.05 -0.00 -0.00 + -0.00000000 0.00000032 0.00000000 -0.00 0.05 0.00 + -0.00000000 0.00000000 0.00000032 -0.00 0.00 0.05 + + + Writing output data file Si.save + + init_run : 0.06s CPU 0.23s WALL ( 1 calls) + electrons : 0.85s CPU 1.01s WALL ( 1 calls) + forces : 0.00s CPU 0.01s WALL ( 1 calls) + stress : 0.02s CPU 0.03s WALL ( 1 calls) + + Called by init_run: + wfcinit : 0.04s CPU 0.11s WALL ( 1 calls) + potinit : 0.00s CPU 0.01s WALL ( 1 calls) + + Called by electrons: + c_bands : 0.73s CPU 0.80s WALL ( 11 calls) + sum_band : 0.11s CPU 0.13s WALL ( 11 calls) + v_of_rho : 0.00s CPU 0.01s WALL ( 11 calls) + mix_rho : 0.00s CPU 0.01s WALL ( 11 calls) + + Called by c_bands: + init_us_2 : 0.01s CPU 0.03s WALL ( 725 calls) + cegterg : 0.69s CPU 0.74s WALL ( 319 calls) + + Called by sum_band: + + Called by *egterg: + h_psi : 0.62s CPU 0.65s WALL ( 980 calls) + g_psi : 0.00s CPU 0.00s WALL ( 632 calls) + cdiaghg : 0.05s CPU 0.10s WALL ( 922 calls) + + Called by h_psi: + h_psi:pot : 0.61s CPU 0.65s WALL ( 980 calls) + h_psi:calbec : 0.03s CPU 0.04s WALL ( 980 calls) + vloc_psi : 0.57s CPU 0.59s WALL ( 980 calls) + add_vuspsi : 0.01s CPU 0.01s WALL ( 980 calls) + + General routines + calbec : 0.03s CPU 0.05s WALL ( 1125 calls) + fft : 0.01s CPU 0.05s WALL ( 50 calls) + fftw : 0.57s CPU 0.64s WALL ( 8656 calls) + davcio : 0.00s CPU 0.06s WALL ( 29 calls) + + Parallel routines + fft_scatter : 0.29s CPU 0.31s WALL ( 8706 calls) + + PWSCF : 1.07s CPU 2.22s WALL + + + This run was terminated on: 19:30: 3 27Sep2017 + +=------------------------------------------------------------------------------= + JOB DONE. +=------------------------------------------------------------------------------= diff --git a/capolanco/test.scf2.in b/capolanco/test.scf2.in new file mode 100644 index 00000000..529f9f22 --- /dev/null +++ b/capolanco/test.scf2.in @@ -0,0 +1,30 @@ + &control + calculation='scf', + outdir = '/global/cscratch1/sd/cpolanco/Si/', + prefix='Si', + pseudo_dir = '/global/homes/c/cpolanco/Materials/pseudo/', + restart_mode='from_scratch', + tprnfor= .true., + tstress= .true., + / + &system + ibrav= 2, + celldm(1)= 10.20777693, + nat= 2, + ntyp= 1, + ecutwfc= 100.0 + / + &electrons + mixing_beta= 0.7 + conv_thr= 1.0d-14 + / + +ATOMIC_SPECIES + Si 28.086 Si.pz-vbc.UPF + +ATOMIC_POSITIONS (alat) + Si 0.00 0.00 0.00 + Si 0.25 0.25 0.25 + +K_POINTS (automatic) + 12 12 12 0 0 0 \ No newline at end of file diff --git a/capolanco/test.scf2.out b/capolanco/test.scf2.out new file mode 100644 index 00000000..ce5f954a --- /dev/null +++ b/capolanco/test.scf2.out @@ -0,0 +1,437 @@ + + Program PWSCF v.6.1 starts on 27Sep2017 at 19:30: 1 + + This program is part of the open-source Quantum ESPRESSO suite + for quantum simulation of materials; please cite + "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); + URL http://www.quantum-espresso.org", + in publications or presentations arising from this work. More details at + http://www.quantum-espresso.org/quote + + Parallel version (MPI & OpenMP), running on 24 processor cores + Number of MPI processes: 24 + Threads/MPI process: 1 + R & G space division: proc/nbgrp/npool/nimage = 24 + Waiting for input... + Reading input from standard input + + Current dimensions of program PWSCF are: + Max number of different atomic species (ntypx) = 10 + Max number of k-points (npk) = 40000 + Max angular momentum in pseudopotentials (lmaxx) = 3 + + Subspace diagonalization in iterative solution of the eigenvalue problem: + a serial algorithm will be used + + + Parallelization info + -------------------- + sticks: dense smooth PW G-vecs: dense smooth PW + Min 59 59 17 1489 1489 232 + Max 60 60 18 1494 1494 235 + Sum 1417 1417 421 35749 35749 5601 + + + + bravais-lattice index = 2 + lattice parameter (alat) = 10.2078 a.u. + unit-cell volume = 265.9093 (a.u.)^3 + number of atoms/cell = 2 + number of atomic types = 1 + number of electrons = 8.00 + number of Kohn-Sham states= 4 + kinetic-energy cutoff = 100.0000 Ry + charge density cutoff = 400.0000 Ry + convergence threshold = 1.0E-14 + mixing beta = 0.7000 + number of iterations used = 8 plain mixing + Exchange-correlation = SLA PZ NOGX NOGC ( 1 1 0 0 0 0) + + celldm(1)= 10.207777 celldm(2)= 0.000000 celldm(3)= 0.000000 + celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000 + + crystal axes: (cart. coord. in units of alat) + a(1) = ( -0.500000 0.000000 0.500000 ) + a(2) = ( 0.000000 0.500000 0.500000 ) + a(3) = ( -0.500000 0.500000 0.000000 ) + + reciprocal axes: (cart. coord. in units 2 pi/alat) + b(1) = ( -1.000000 -1.000000 1.000000 ) + b(2) = ( 1.000000 1.000000 1.000000 ) + b(3) = ( -1.000000 1.000000 -1.000000 ) + + + PseudoPot. # 1 for Si read from file: + /global/homes/c/cpolanco/Materials/pseudo/Si.pz-vbc.UPF + MD5 check sum: 6dfa03ddd5817404712e03e4d12deb78 + Pseudo is Norm-conserving, Zval = 4.0 + Generated by new atomic code, or converted to UPF format + Using radial grid of 431 points, 2 beta functions with: + l(1) = 0 + l(2) = 1 + + atomic species valence mass pseudopotential + Si 4.00 28.08600 Si( 1.00) + + 24 Sym. Ops. (no inversion) found + (note: 24 additional sym.ops. were found but ignored + their fractional translations are incommensurate with FFT grid) + + + Cartesian axes + + site n. atom positions (alat units) + 1 Si tau( 1) = ( 0.0000000 0.0000000 0.0000000 ) + 2 Si tau( 2) = ( 0.2500000 0.2500000 0.2500000 ) + + number of k points= 29 + cart. coord. in units 2pi/alat + k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 0.0039062 + k( 2) = ( -0.1250000 0.1250000 -0.1250000), wk = 0.0312500 + k( 3) = ( -0.2500000 0.2500000 -0.2500000), wk = 0.0312500 + k( 4) = ( -0.3750000 0.3750000 -0.3750000), wk = 0.0312500 + k( 5) = ( 0.5000000 -0.5000000 0.5000000), wk = 0.0156250 + k( 6) = ( 0.0000000 0.2500000 0.0000000), wk = 0.0234375 + k( 7) = ( -0.1250000 0.3750000 -0.1250000), wk = 0.0937500 + k( 8) = ( -0.2500000 0.5000000 -0.2500000), wk = 0.0937500 + k( 9) = ( 0.6250000 -0.3750000 0.6250000), wk = 0.0937500 + k( 10) = ( 0.5000000 -0.2500000 0.5000000), wk = 0.0937500 + k( 11) = ( 0.3750000 -0.1250000 0.3750000), wk = 0.0937500 + k( 12) = ( 0.2500000 0.0000000 0.2500000), wk = 0.0468750 + k( 13) = ( 0.0000000 0.5000000 0.0000000), wk = 0.0234375 + k( 14) = ( -0.1250000 0.6250000 -0.1250000), wk = 0.0937500 + k( 15) = ( 0.7500000 -0.2500000 0.7500000), wk = 0.0937500 + k( 16) = ( 0.6250000 -0.1250000 0.6250000), wk = 0.0937500 + k( 17) = ( 0.5000000 0.0000000 0.5000000), wk = 0.0468750 + k( 18) = ( 0.0000000 0.7500000 0.0000000), wk = 0.0234375 + k( 19) = ( 0.8750000 -0.1250000 0.8750000), wk = 0.0937500 + k( 20) = ( 0.7500000 0.0000000 0.7500000), wk = 0.0468750 + k( 21) = ( 0.0000000 -1.0000000 0.0000000), wk = 0.0117188 + k( 22) = ( -0.2500000 0.5000000 0.0000000), wk = 0.0937500 + k( 23) = ( 0.6250000 -0.3750000 0.8750000), wk = 0.1875000 + k( 24) = ( 0.5000000 -0.2500000 0.7500000), wk = 0.0937500 + k( 25) = ( 0.7500000 -0.2500000 1.0000000), wk = 0.0937500 + k( 26) = ( 0.6250000 -0.1250000 0.8750000), wk = 0.1875000 + k( 27) = ( 0.5000000 0.0000000 0.7500000), wk = 0.0937500 + k( 28) = ( -0.2500000 -1.0000000 0.0000000), wk = 0.0468750 + k( 29) = ( -0.5000000 -1.0000000 0.0000000), wk = 0.0234375 + + Dense grid: 35749 G-vectors FFT dimensions: ( 45, 45, 45) + + Estimated max dynamical RAM per process > 1.29MB + + Estimated total allocated dynamical RAM > 31.06MB + + Initial potential from superposition of free atoms + + starting charge 7.99901, renormalised to 8.00000 + Starting wfc are 8 randomized atomic wfcs + + total cpu time spent up to now is 0.4 secs + + per-process dynamical memory: 2.9 Mb + + Self-consistent Calculation + + iteration # 1 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.00E-02, avg # of iterations = 2.0 + + Threshold (ethr) on eigenvalues was too large: + Diagonalizing with lowered threshold + + Davidson diagonalization with overlap + ethr = 7.97E-04, avg # of iterations = 1.0 + + total cpu time spent up to now is 0.6 secs + + total energy = -15.84982619 Ry + Harris-Foulkes estimate = -15.87079416 Ry + estimated scf accuracy < 0.06161703 Ry + + iteration # 2 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 7.70E-04, avg # of iterations = 1.0 + + total cpu time spent up to now is 0.7 secs + + total energy = -15.85288351 Ry + Harris-Foulkes estimate = -15.85318795 Ry + estimated scf accuracy < 0.00216687 Ry + + iteration # 3 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 2.71E-05, avg # of iterations = 2.4 + + total cpu time spent up to now is 0.8 secs + + total energy = -15.85332918 Ry + Harris-Foulkes estimate = -15.85336185 Ry + estimated scf accuracy < 0.00007437 Ry + + iteration # 4 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 9.30E-07, avg # of iterations = 2.1 + + total cpu time spent up to now is 0.8 secs + + total energy = -15.85334986 Ry + Harris-Foulkes estimate = -15.85335396 Ry + estimated scf accuracy < 0.00000888 Ry + + iteration # 5 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.11E-07, avg # of iterations = 2.1 + + total cpu time spent up to now is 0.9 secs + + total energy = -15.85335134 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 0.00000011 Ry + + iteration # 6 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.35E-09, avg # of iterations = 2.6 + + total cpu time spent up to now is 1.0 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 2.9E-09 Ry + + iteration # 7 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 3.68E-11, avg # of iterations = 2.6 + + total cpu time spent up to now is 1.1 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 2.9E-11 Ry + + iteration # 8 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 3.65E-13, avg # of iterations = 3.3 + + total cpu time spent up to now is 1.2 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 5.4E-12 Ry + + iteration # 9 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.00E-13, avg # of iterations = 1.7 + + total cpu time spent up to now is 1.3 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 1.2E-13 Ry + + iteration # 10 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.00E-13, avg # of iterations = 1.0 + + total cpu time spent up to now is 1.4 secs + + End of self-consistent calculation + + k = 0.0000 0.0000 0.0000 ( 4477 PWs) bands (ev): + + -5.8300 6.2061 6.2061 6.2061 + + k =-0.1250 0.1250-0.1250 ( 4507 PWs) bands (ev): + + -5.6230 4.6051 5.9132 5.9132 + + k =-0.2500 0.2500-0.2500 ( 4510 PWs) bands (ev): + + -5.0182 2.2559 5.4373 5.4373 + + k =-0.3750 0.3750-0.3750 ( 4501 PWs) bands (ev): + + -4.1058 0.2065 5.1074 5.1074 + + k = 0.5000-0.5000 0.5000 ( 4476 PWs) bands (ev): + + -3.4453 -0.8427 4.9947 4.9947 + + k = 0.0000 0.2500 0.0000 ( 4504 PWs) bands (ev): + + -5.5533 4.8935 5.3857 5.3857 + + k =-0.1250 0.3750-0.1250 ( 4517 PWs) bands (ev): + + -5.0777 2.9801 4.8669 4.9518 + + k =-0.2500 0.5000-0.2500 ( 4508 PWs) bands (ev): + + -4.2481 0.8896 4.3532 4.5964 + + k = 0.6250-0.3750 0.6250 ( 4486 PWs) bands (ev): + + -3.3613 -0.6068 3.9003 4.6231 + + k = 0.5000-0.2500 0.5000 ( 4491 PWs) bands (ev): + + -3.6148 -0.2257 3.7125 4.9256 + + k = 0.3750-0.1250 0.3750 ( 4497 PWs) bands (ev): + + -4.5602 1.5598 3.8591 5.4251 + + k = 0.2500 0.0000 0.2500 ( 4477 PWs) bands (ev): + + -5.2819 3.5267 4.5444 5.9125 + + k = 0.0000 0.5000 0.0000 ( 4520 PWs) bands (ev): + + -4.7329 2.7148 4.2862 4.2862 + + k =-0.1250 0.6250-0.1250 ( 4509 PWs) bands (ev): + + -4.0117 1.2745 3.4881 3.9636 + + k = 0.7500-0.2500 0.7500 ( 4482 PWs) bands (ev): + + -3.0647 -0.1975 2.6082 3.9678 + + k = 0.6250-0.1250 0.6250 ( 4477 PWs) bands (ev): + + -2.8512 -0.4657 2.1376 4.2926 + + k = 0.5000 0.0000 0.5000 ( 4489 PWs) bands (ev): + + -3.7521 0.7207 2.3750 4.8614 + + k = 0.0000 0.7500 0.0000 ( 4484 PWs) bands (ev): + + -3.4015 0.4708 3.5586 3.5586 + + k = 0.8750-0.1250 0.8750 ( 4479 PWs) bands (ev): + + -2.4888 -0.6253 2.7002 3.4815 + + k = 0.7500 0.0000 0.7500 ( 4454 PWs) bands (ev): + + -2.0305 -1.0339 1.8049 3.7440 + + k = 0.0000-1.0000 0.0000 ( 4456 PWs) bands (ev): + + -1.6267 -1.6267 3.3090 3.3090 + + k =-0.2500 0.5000 0.0000 ( 4503 PWs) bands (ev): + + -4.4807 1.9234 3.4393 4.7592 + + k = 0.6250-0.3750 0.8750 ( 4489 PWs) bands (ev): + + -3.5748 0.3447 2.8290 4.2439 + + k = 0.5000-0.2500 0.7500 ( 4486 PWs) bands (ev): + + -2.9014 -0.6278 2.7039 4.0076 + + k = 0.7500-0.2500 1.0000 ( 4484 PWs) bands (ev): + + -3.1970 0.2501 2.7770 3.3923 + + k = 0.6250-0.1250 0.8750 ( 4486 PWs) bands (ev): + + -2.3006 -0.7332 2.0576 3.1860 + + k = 0.5000 0.0000 0.7500 ( 4490 PWs) bands (ev): + + -2.6570 -0.3670 1.8851 3.5717 + + k =-0.2500-1.0000 0.0000 ( 4472 PWs) bands (ev): + + -1.5427 -1.5427 2.7194 2.7194 + + k =-0.5000-1.0000 0.0000 ( 4488 PWs) bands (ev): + + -1.4495 -1.4495 2.2655 2.2655 + + highest occupied level (ev): 6.2061 + +! total energy = -15.95335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 4.0E-15 Ry + + The total energy is the sum of the following terms: + + one-electron contribution = 4.76680131 Ry + hartree contribution = 1.08149972 Ry + xc contribution = -4.81476914 Ry + ewald contribution = -16.88688327 Ry + + convergence has been achieved in 10 iterations + + Forces acting on atoms (cartesian axes, Ry/au): + + atom 1 type 1 force = 0.00000000 0.00000000 0.00000000 + atom 2 type 1 force = 0.00000000 0.00000000 -0.00000000 + + Total force = 0.000000 Total SCF correction = 0.000000 + + + Computing stress (Cartesian axis) and pressure + + total stress (Ry/bohr**3) (kbar) P= 0.05 + 0.00000032 -0.00000000 -0.00000000 0.05 -0.00 -0.00 + -0.00000000 0.00000032 0.00000000 -0.00 0.05 0.00 + -0.00000000 0.00000000 0.00000032 -0.00 0.00 0.05 + + + Writing output data file Si.save + + init_run : 0.06s CPU 0.23s WALL ( 1 calls) + electrons : 0.85s CPU 1.01s WALL ( 1 calls) + forces : 0.00s CPU 0.01s WALL ( 1 calls) + stress : 0.02s CPU 0.03s WALL ( 1 calls) + + Called by init_run: + wfcinit : 0.04s CPU 0.11s WALL ( 1 calls) + potinit : 0.00s CPU 0.01s WALL ( 1 calls) + + Called by electrons: + c_bands : 0.73s CPU 0.80s WALL ( 11 calls) + sum_band : 0.11s CPU 0.13s WALL ( 11 calls) + v_of_rho : 0.00s CPU 0.01s WALL ( 11 calls) + mix_rho : 0.00s CPU 0.01s WALL ( 11 calls) + + Called by c_bands: + init_us_2 : 0.01s CPU 0.03s WALL ( 725 calls) + cegterg : 0.69s CPU 0.74s WALL ( 319 calls) + + Called by sum_band: + + Called by *egterg: + h_psi : 0.62s CPU 0.65s WALL ( 980 calls) + g_psi : 0.00s CPU 0.00s WALL ( 632 calls) + cdiaghg : 0.05s CPU 0.10s WALL ( 922 calls) + + Called by h_psi: + h_psi:pot : 0.61s CPU 0.65s WALL ( 980 calls) + h_psi:calbec : 0.03s CPU 0.04s WALL ( 980 calls) + vloc_psi : 0.57s CPU 0.59s WALL ( 980 calls) + add_vuspsi : 0.01s CPU 0.01s WALL ( 980 calls) + + General routines + calbec : 0.03s CPU 0.05s WALL ( 1125 calls) + fft : 0.01s CPU 0.05s WALL ( 50 calls) + fftw : 0.57s CPU 0.64s WALL ( 8656 calls) + davcio : 0.00s CPU 0.06s WALL ( 29 calls) + + Parallel routines + fft_scatter : 0.29s CPU 0.31s WALL ( 8706 calls) + + PWSCF : 1.07s CPU 2.22s WALL + + + This run was terminated on: 19:30: 3 27Sep2017 + +=------------------------------------------------------------------------------= + JOB DONE. +=------------------------------------------------------------------------------= diff --git a/capolanco/test.scf3.in b/capolanco/test.scf3.in new file mode 100644 index 00000000..ef5210f4 --- /dev/null +++ b/capolanco/test.scf3.in @@ -0,0 +1,30 @@ + &control + calculation='scf', + outdir = '/global/cscratch1/sd/cpolanco/Si/', + prefix='Si', + pseudo_dir = '/global/homes/c/cpolanco/Materials/pseudo/', + restart_mode='from_scratch', + tprnfor= .true., + tstress= .true., + / + &system + ibrav= 2, + celldm(1)= 10.20777693, + nat= 2, + ntyp= 1, + ecutwfc= 100.0 + / + &electrons + mixing_beta= 0.7 + conv_thr= 1.0d-14 + / + +ATOMIC_SPECIES + Si 28.086 Si.pz-vbc.UPF + +ATOMIC_POSITIONS (alat) + Si 0.00 0.00 0.00 + Si 0.25 0.25 0.25 + +K_POINTS (automatic) + 14 14 14 0 0 0 \ No newline at end of file diff --git a/capolanco/test.scf3.out b/capolanco/test.scf3.out new file mode 100644 index 00000000..24c158b7 --- /dev/null +++ b/capolanco/test.scf3.out @@ -0,0 +1,437 @@ + + Program PWSCF v.6.1 starts on 27Sep2017 at 19:30: 1 + + This program is part of the open-source Quantum ESPRESSO suite + for quantum simulation of materials; please cite + "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); + URL http://www.quantum-espresso.org", + in publications or presentations arising from this work. More details at + http://www.quantum-espresso.org/quote + + Parallel version (MPI & OpenMP), running on 24 processor cores + Number of MPI processes: 24 + Threads/MPI process: 1 + R & G space division: proc/nbgrp/npool/nimage = 24 + Waiting for input... + Reading input from standard input + + Current dimensions of program PWSCF are: + Max number of different atomic species (ntypx) = 10 + Max number of k-points (npk) = 40000 + Max angular momentum in pseudopotentials (lmaxx) = 3 + + Subspace diagonalization in iterative solution of the eigenvalue problem: + a serial algorithm will be used + + + Parallelization info + -------------------- + sticks: dense smooth PW G-vecs: dense smooth PW + Min 59 59 17 1489 1489 232 + Max 60 60 18 1494 1494 235 + Sum 1417 1417 421 35749 35749 5601 + + + + bravais-lattice index = 2 + lattice parameter (alat) = 10.2078 a.u. + unit-cell volume = 265.9093 (a.u.)^3 + number of atoms/cell = 2 + number of atomic types = 1 + number of electrons = 8.00 + number of Kohn-Sham states= 4 + kinetic-energy cutoff = 100.0000 Ry + charge density cutoff = 400.0000 Ry + convergence threshold = 1.0E-14 + mixing beta = 0.7000 + number of iterations used = 8 plain mixing + Exchange-correlation = SLA PZ NOGX NOGC ( 1 1 0 0 0 0) + + celldm(1)= 10.207777 celldm(2)= 0.000000 celldm(3)= 0.000000 + celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000 + + crystal axes: (cart. coord. in units of alat) + a(1) = ( -0.500000 0.000000 0.500000 ) + a(2) = ( 0.000000 0.500000 0.500000 ) + a(3) = ( -0.500000 0.500000 0.000000 ) + + reciprocal axes: (cart. coord. in units 2 pi/alat) + b(1) = ( -1.000000 -1.000000 1.000000 ) + b(2) = ( 1.000000 1.000000 1.000000 ) + b(3) = ( -1.000000 1.000000 -1.000000 ) + + + PseudoPot. # 1 for Si read from file: + /global/homes/c/cpolanco/Materials/pseudo/Si.pz-vbc.UPF + MD5 check sum: 6dfa03ddd5817404712e03e4d12deb78 + Pseudo is Norm-conserving, Zval = 4.0 + Generated by new atomic code, or converted to UPF format + Using radial grid of 431 points, 2 beta functions with: + l(1) = 0 + l(2) = 1 + + atomic species valence mass pseudopotential + Si 4.00 28.08600 Si( 1.00) + + 24 Sym. Ops. (no inversion) found + (note: 24 additional sym.ops. were found but ignored + their fractional translations are incommensurate with FFT grid) + + + Cartesian axes + + site n. atom positions (alat units) + 1 Si tau( 1) = ( 0.0000000 0.0000000 0.0000000 ) + 2 Si tau( 2) = ( 0.2500000 0.2500000 0.2500000 ) + + number of k points= 29 + cart. coord. in units 2pi/alat + k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 0.0039062 + k( 2) = ( -0.1250000 0.1250000 -0.1250000), wk = 0.0312500 + k( 3) = ( -0.2500000 0.2500000 -0.2500000), wk = 0.0312500 + k( 4) = ( -0.3750000 0.3750000 -0.3750000), wk = 0.0312500 + k( 5) = ( 0.5000000 -0.5000000 0.5000000), wk = 0.0156250 + k( 6) = ( 0.0000000 0.2500000 0.0000000), wk = 0.0234375 + k( 7) = ( -0.1250000 0.3750000 -0.1250000), wk = 0.0937500 + k( 8) = ( -0.2500000 0.5000000 -0.2500000), wk = 0.0937500 + k( 9) = ( 0.6250000 -0.3750000 0.6250000), wk = 0.0937500 + k( 10) = ( 0.5000000 -0.2500000 0.5000000), wk = 0.0937500 + k( 11) = ( 0.3750000 -0.1250000 0.3750000), wk = 0.0937500 + k( 12) = ( 0.2500000 0.0000000 0.2500000), wk = 0.0468750 + k( 13) = ( 0.0000000 0.5000000 0.0000000), wk = 0.0234375 + k( 14) = ( -0.1250000 0.6250000 -0.1250000), wk = 0.0937500 + k( 15) = ( 0.7500000 -0.2500000 0.7500000), wk = 0.0937500 + k( 16) = ( 0.6250000 -0.1250000 0.6250000), wk = 0.0937500 + k( 17) = ( 0.5000000 0.0000000 0.5000000), wk = 0.0468750 + k( 18) = ( 0.0000000 0.7500000 0.0000000), wk = 0.0234375 + k( 19) = ( 0.8750000 -0.1250000 0.8750000), wk = 0.0937500 + k( 20) = ( 0.7500000 0.0000000 0.7500000), wk = 0.0468750 + k( 21) = ( 0.0000000 -1.0000000 0.0000000), wk = 0.0117188 + k( 22) = ( -0.2500000 0.5000000 0.0000000), wk = 0.0937500 + k( 23) = ( 0.6250000 -0.3750000 0.8750000), wk = 0.1875000 + k( 24) = ( 0.5000000 -0.2500000 0.7500000), wk = 0.0937500 + k( 25) = ( 0.7500000 -0.2500000 1.0000000), wk = 0.0937500 + k( 26) = ( 0.6250000 -0.1250000 0.8750000), wk = 0.1875000 + k( 27) = ( 0.5000000 0.0000000 0.7500000), wk = 0.0937500 + k( 28) = ( -0.2500000 -1.0000000 0.0000000), wk = 0.0468750 + k( 29) = ( -0.5000000 -1.0000000 0.0000000), wk = 0.0234375 + + Dense grid: 35749 G-vectors FFT dimensions: ( 45, 45, 45) + + Estimated max dynamical RAM per process > 1.29MB + + Estimated total allocated dynamical RAM > 31.06MB + + Initial potential from superposition of free atoms + + starting charge 7.99901, renormalised to 8.00000 + Starting wfc are 8 randomized atomic wfcs + + total cpu time spent up to now is 0.4 secs + + per-process dynamical memory: 2.9 Mb + + Self-consistent Calculation + + iteration # 1 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.00E-02, avg # of iterations = 2.0 + + Threshold (ethr) on eigenvalues was too large: + Diagonalizing with lowered threshold + + Davidson diagonalization with overlap + ethr = 7.97E-04, avg # of iterations = 1.0 + + total cpu time spent up to now is 0.6 secs + + total energy = -15.84982619 Ry + Harris-Foulkes estimate = -15.87079416 Ry + estimated scf accuracy < 0.06161703 Ry + + iteration # 2 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 7.70E-04, avg # of iterations = 1.0 + + total cpu time spent up to now is 0.7 secs + + total energy = -15.85288351 Ry + Harris-Foulkes estimate = -15.85318795 Ry + estimated scf accuracy < 0.00216687 Ry + + iteration # 3 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 2.71E-05, avg # of iterations = 2.4 + + total cpu time spent up to now is 0.8 secs + + total energy = -15.85332918 Ry + Harris-Foulkes estimate = -15.85336185 Ry + estimated scf accuracy < 0.00007437 Ry + + iteration # 4 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 9.30E-07, avg # of iterations = 2.1 + + total cpu time spent up to now is 0.8 secs + + total energy = -15.85334986 Ry + Harris-Foulkes estimate = -15.85335396 Ry + estimated scf accuracy < 0.00000888 Ry + + iteration # 5 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.11E-07, avg # of iterations = 2.1 + + total cpu time spent up to now is 0.9 secs + + total energy = -15.85335134 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 0.00000011 Ry + + iteration # 6 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.35E-09, avg # of iterations = 2.6 + + total cpu time spent up to now is 1.0 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 2.9E-09 Ry + + iteration # 7 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 3.68E-11, avg # of iterations = 2.6 + + total cpu time spent up to now is 1.1 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 2.9E-11 Ry + + iteration # 8 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 3.65E-13, avg # of iterations = 3.3 + + total cpu time spent up to now is 1.2 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 5.4E-12 Ry + + iteration # 9 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.00E-13, avg # of iterations = 1.7 + + total cpu time spent up to now is 1.3 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 1.2E-13 Ry + + iteration # 10 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.00E-13, avg # of iterations = 1.0 + + total cpu time spent up to now is 1.4 secs + + End of self-consistent calculation + + k = 0.0000 0.0000 0.0000 ( 4477 PWs) bands (ev): + + -5.8300 6.2061 6.2061 6.2061 + + k =-0.1250 0.1250-0.1250 ( 4507 PWs) bands (ev): + + -5.6230 4.6051 5.9132 5.9132 + + k =-0.2500 0.2500-0.2500 ( 4510 PWs) bands (ev): + + -5.0182 2.2559 5.4373 5.4373 + + k =-0.3750 0.3750-0.3750 ( 4501 PWs) bands (ev): + + -4.1058 0.2065 5.1074 5.1074 + + k = 0.5000-0.5000 0.5000 ( 4476 PWs) bands (ev): + + -3.4453 -0.8427 4.9947 4.9947 + + k = 0.0000 0.2500 0.0000 ( 4504 PWs) bands (ev): + + -5.5533 4.8935 5.3857 5.3857 + + k =-0.1250 0.3750-0.1250 ( 4517 PWs) bands (ev): + + -5.0777 2.9801 4.8669 4.9518 + + k =-0.2500 0.5000-0.2500 ( 4508 PWs) bands (ev): + + -4.2481 0.8896 4.3532 4.5964 + + k = 0.6250-0.3750 0.6250 ( 4486 PWs) bands (ev): + + -3.3613 -0.6068 3.9003 4.6231 + + k = 0.5000-0.2500 0.5000 ( 4491 PWs) bands (ev): + + -3.6148 -0.2257 3.7125 4.9256 + + k = 0.3750-0.1250 0.3750 ( 4497 PWs) bands (ev): + + -4.5602 1.5598 3.8591 5.4251 + + k = 0.2500 0.0000 0.2500 ( 4477 PWs) bands (ev): + + -5.2819 3.5267 4.5444 5.9125 + + k = 0.0000 0.5000 0.0000 ( 4520 PWs) bands (ev): + + -4.7329 2.7148 4.2862 4.2862 + + k =-0.1250 0.6250-0.1250 ( 4509 PWs) bands (ev): + + -4.0117 1.2745 3.4881 3.9636 + + k = 0.7500-0.2500 0.7500 ( 4482 PWs) bands (ev): + + -3.0647 -0.1975 2.6082 3.9678 + + k = 0.6250-0.1250 0.6250 ( 4477 PWs) bands (ev): + + -2.8512 -0.4657 2.1376 4.2926 + + k = 0.5000 0.0000 0.5000 ( 4489 PWs) bands (ev): + + -3.7521 0.7207 2.3750 4.8614 + + k = 0.0000 0.7500 0.0000 ( 4484 PWs) bands (ev): + + -3.4015 0.4708 3.5586 3.5586 + + k = 0.8750-0.1250 0.8750 ( 4479 PWs) bands (ev): + + -2.4888 -0.6253 2.7002 3.4815 + + k = 0.7500 0.0000 0.7500 ( 4454 PWs) bands (ev): + + -2.0305 -1.0339 1.8049 3.7440 + + k = 0.0000-1.0000 0.0000 ( 4456 PWs) bands (ev): + + -1.6267 -1.6267 3.3090 3.3090 + + k =-0.2500 0.5000 0.0000 ( 4503 PWs) bands (ev): + + -4.4807 1.9234 3.4393 4.7592 + + k = 0.6250-0.3750 0.8750 ( 4489 PWs) bands (ev): + + -3.5748 0.3447 2.8290 4.2439 + + k = 0.5000-0.2500 0.7500 ( 4486 PWs) bands (ev): + + -2.9014 -0.6278 2.7039 4.0076 + + k = 0.7500-0.2500 1.0000 ( 4484 PWs) bands (ev): + + -3.1970 0.2501 2.7770 3.3923 + + k = 0.6250-0.1250 0.8750 ( 4486 PWs) bands (ev): + + -2.3006 -0.7332 2.0576 3.1860 + + k = 0.5000 0.0000 0.7500 ( 4490 PWs) bands (ev): + + -2.6570 -0.3670 1.8851 3.5717 + + k =-0.2500-1.0000 0.0000 ( 4472 PWs) bands (ev): + + -1.5427 -1.5427 2.7194 2.7194 + + k =-0.5000-1.0000 0.0000 ( 4488 PWs) bands (ev): + + -1.4495 -1.4495 2.2655 2.2655 + + highest occupied level (ev): 6.2061 + +! total energy = -15.86335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 4.0E-15 Ry + + The total energy is the sum of the following terms: + + one-electron contribution = 4.76680131 Ry + hartree contribution = 1.08149972 Ry + xc contribution = -4.81476914 Ry + ewald contribution = -16.88688327 Ry + + convergence has been achieved in 10 iterations + + Forces acting on atoms (cartesian axes, Ry/au): + + atom 1 type 1 force = 0.00000000 0.00000000 0.00000000 + atom 2 type 1 force = 0.00000000 0.00000000 -0.00000000 + + Total force = 0.000000 Total SCF correction = 0.000000 + + + Computing stress (Cartesian axis) and pressure + + total stress (Ry/bohr**3) (kbar) P= 0.05 + 0.00000032 -0.00000000 -0.00000000 0.05 -0.00 -0.00 + -0.00000000 0.00000032 0.00000000 -0.00 0.05 0.00 + -0.00000000 0.00000000 0.00000032 -0.00 0.00 0.05 + + + Writing output data file Si.save + + init_run : 0.06s CPU 0.23s WALL ( 1 calls) + electrons : 0.85s CPU 1.01s WALL ( 1 calls) + forces : 0.00s CPU 0.01s WALL ( 1 calls) + stress : 0.02s CPU 0.03s WALL ( 1 calls) + + Called by init_run: + wfcinit : 0.04s CPU 0.11s WALL ( 1 calls) + potinit : 0.00s CPU 0.01s WALL ( 1 calls) + + Called by electrons: + c_bands : 0.73s CPU 0.80s WALL ( 11 calls) + sum_band : 0.11s CPU 0.13s WALL ( 11 calls) + v_of_rho : 0.00s CPU 0.01s WALL ( 11 calls) + mix_rho : 0.00s CPU 0.01s WALL ( 11 calls) + + Called by c_bands: + init_us_2 : 0.01s CPU 0.03s WALL ( 725 calls) + cegterg : 0.69s CPU 0.74s WALL ( 319 calls) + + Called by sum_band: + + Called by *egterg: + h_psi : 0.62s CPU 0.65s WALL ( 980 calls) + g_psi : 0.00s CPU 0.00s WALL ( 632 calls) + cdiaghg : 0.05s CPU 0.10s WALL ( 922 calls) + + Called by h_psi: + h_psi:pot : 0.61s CPU 0.65s WALL ( 980 calls) + h_psi:calbec : 0.03s CPU 0.04s WALL ( 980 calls) + vloc_psi : 0.57s CPU 0.59s WALL ( 980 calls) + add_vuspsi : 0.01s CPU 0.01s WALL ( 980 calls) + + General routines + calbec : 0.03s CPU 0.05s WALL ( 1125 calls) + fft : 0.01s CPU 0.05s WALL ( 50 calls) + fftw : 0.57s CPU 0.64s WALL ( 8656 calls) + davcio : 0.00s CPU 0.06s WALL ( 29 calls) + + Parallel routines + fft_scatter : 0.29s CPU 0.31s WALL ( 8706 calls) + + PWSCF : 1.07s CPU 2.22s WALL + + + This run was terminated on: 19:30: 3 27Sep2017 + +=------------------------------------------------------------------------------= + JOB DONE. +=------------------------------------------------------------------------------= diff --git a/capolanco/test.scf4.in b/capolanco/test.scf4.in new file mode 100644 index 00000000..34dccffe --- /dev/null +++ b/capolanco/test.scf4.in @@ -0,0 +1,30 @@ + &control + calculation='scf', + outdir = '/global/cscratch1/sd/cpolanco/Si/', + prefix='Si', + pseudo_dir = '/global/homes/c/cpolanco/Materials/pseudo/', + restart_mode='from_scratch', + tprnfor= .true., + tstress= .true., + / + &system + ibrav= 2, + celldm(1)= 10.20777693, + nat= 2, + ntyp= 1, + ecutwfc= 100.0 + / + &electrons + mixing_beta= 0.7 + conv_thr= 1.0d-14 + / + +ATOMIC_SPECIES + Si 28.086 Si.pz-vbc.UPF + +ATOMIC_POSITIONS (alat) + Si 0.00 0.00 0.00 + Si 0.25 0.25 0.25 + +K_POINTS (automatic) + 16 16 16 0 0 0 \ No newline at end of file diff --git a/capolanco/test.scf4.out b/capolanco/test.scf4.out new file mode 100644 index 00000000..c777d624 --- /dev/null +++ b/capolanco/test.scf4.out @@ -0,0 +1,437 @@ + + Program PWSCF v.6.1 starts on 27Sep2017 at 19:30: 1 + + This program is part of the open-source Quantum ESPRESSO suite + for quantum simulation of materials; please cite + "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); + URL http://www.quantum-espresso.org", + in publications or presentations arising from this work. More details at + http://www.quantum-espresso.org/quote + + Parallel version (MPI & OpenMP), running on 24 processor cores + Number of MPI processes: 24 + Threads/MPI process: 1 + R & G space division: proc/nbgrp/npool/nimage = 24 + Waiting for input... + Reading input from standard input + + Current dimensions of program PWSCF are: + Max number of different atomic species (ntypx) = 10 + Max number of k-points (npk) = 40000 + Max angular momentum in pseudopotentials (lmaxx) = 3 + + Subspace diagonalization in iterative solution of the eigenvalue problem: + a serial algorithm will be used + + + Parallelization info + -------------------- + sticks: dense smooth PW G-vecs: dense smooth PW + Min 59 59 17 1489 1489 232 + Max 60 60 18 1494 1494 235 + Sum 1417 1417 421 35749 35749 5601 + + + + bravais-lattice index = 2 + lattice parameter (alat) = 10.2078 a.u. + unit-cell volume = 265.9093 (a.u.)^3 + number of atoms/cell = 2 + number of atomic types = 1 + number of electrons = 8.00 + number of Kohn-Sham states= 4 + kinetic-energy cutoff = 100.0000 Ry + charge density cutoff = 400.0000 Ry + convergence threshold = 1.0E-14 + mixing beta = 0.7000 + number of iterations used = 8 plain mixing + Exchange-correlation = SLA PZ NOGX NOGC ( 1 1 0 0 0 0) + + celldm(1)= 10.207777 celldm(2)= 0.000000 celldm(3)= 0.000000 + celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000 + + crystal axes: (cart. coord. in units of alat) + a(1) = ( -0.500000 0.000000 0.500000 ) + a(2) = ( 0.000000 0.500000 0.500000 ) + a(3) = ( -0.500000 0.500000 0.000000 ) + + reciprocal axes: (cart. coord. in units 2 pi/alat) + b(1) = ( -1.000000 -1.000000 1.000000 ) + b(2) = ( 1.000000 1.000000 1.000000 ) + b(3) = ( -1.000000 1.000000 -1.000000 ) + + + PseudoPot. # 1 for Si read from file: + /global/homes/c/cpolanco/Materials/pseudo/Si.pz-vbc.UPF + MD5 check sum: 6dfa03ddd5817404712e03e4d12deb78 + Pseudo is Norm-conserving, Zval = 4.0 + Generated by new atomic code, or converted to UPF format + Using radial grid of 431 points, 2 beta functions with: + l(1) = 0 + l(2) = 1 + + atomic species valence mass pseudopotential + Si 4.00 28.08600 Si( 1.00) + + 24 Sym. Ops. (no inversion) found + (note: 24 additional sym.ops. were found but ignored + their fractional translations are incommensurate with FFT grid) + + + Cartesian axes + + site n. atom positions (alat units) + 1 Si tau( 1) = ( 0.0000000 0.0000000 0.0000000 ) + 2 Si tau( 2) = ( 0.2500000 0.2500000 0.2500000 ) + + number of k points= 29 + cart. coord. in units 2pi/alat + k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 0.0039062 + k( 2) = ( -0.1250000 0.1250000 -0.1250000), wk = 0.0312500 + k( 3) = ( -0.2500000 0.2500000 -0.2500000), wk = 0.0312500 + k( 4) = ( -0.3750000 0.3750000 -0.3750000), wk = 0.0312500 + k( 5) = ( 0.5000000 -0.5000000 0.5000000), wk = 0.0156250 + k( 6) = ( 0.0000000 0.2500000 0.0000000), wk = 0.0234375 + k( 7) = ( -0.1250000 0.3750000 -0.1250000), wk = 0.0937500 + k( 8) = ( -0.2500000 0.5000000 -0.2500000), wk = 0.0937500 + k( 9) = ( 0.6250000 -0.3750000 0.6250000), wk = 0.0937500 + k( 10) = ( 0.5000000 -0.2500000 0.5000000), wk = 0.0937500 + k( 11) = ( 0.3750000 -0.1250000 0.3750000), wk = 0.0937500 + k( 12) = ( 0.2500000 0.0000000 0.2500000), wk = 0.0468750 + k( 13) = ( 0.0000000 0.5000000 0.0000000), wk = 0.0234375 + k( 14) = ( -0.1250000 0.6250000 -0.1250000), wk = 0.0937500 + k( 15) = ( 0.7500000 -0.2500000 0.7500000), wk = 0.0937500 + k( 16) = ( 0.6250000 -0.1250000 0.6250000), wk = 0.0937500 + k( 17) = ( 0.5000000 0.0000000 0.5000000), wk = 0.0468750 + k( 18) = ( 0.0000000 0.7500000 0.0000000), wk = 0.0234375 + k( 19) = ( 0.8750000 -0.1250000 0.8750000), wk = 0.0937500 + k( 20) = ( 0.7500000 0.0000000 0.7500000), wk = 0.0468750 + k( 21) = ( 0.0000000 -1.0000000 0.0000000), wk = 0.0117188 + k( 22) = ( -0.2500000 0.5000000 0.0000000), wk = 0.0937500 + k( 23) = ( 0.6250000 -0.3750000 0.8750000), wk = 0.1875000 + k( 24) = ( 0.5000000 -0.2500000 0.7500000), wk = 0.0937500 + k( 25) = ( 0.7500000 -0.2500000 1.0000000), wk = 0.0937500 + k( 26) = ( 0.6250000 -0.1250000 0.8750000), wk = 0.1875000 + k( 27) = ( 0.5000000 0.0000000 0.7500000), wk = 0.0937500 + k( 28) = ( -0.2500000 -1.0000000 0.0000000), wk = 0.0468750 + k( 29) = ( -0.5000000 -1.0000000 0.0000000), wk = 0.0234375 + + Dense grid: 35749 G-vectors FFT dimensions: ( 45, 45, 45) + + Estimated max dynamical RAM per process > 1.29MB + + Estimated total allocated dynamical RAM > 31.06MB + + Initial potential from superposition of free atoms + + starting charge 7.99901, renormalised to 8.00000 + Starting wfc are 8 randomized atomic wfcs + + total cpu time spent up to now is 0.4 secs + + per-process dynamical memory: 2.9 Mb + + Self-consistent Calculation + + iteration # 1 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.00E-02, avg # of iterations = 2.0 + + Threshold (ethr) on eigenvalues was too large: + Diagonalizing with lowered threshold + + Davidson diagonalization with overlap + ethr = 7.97E-04, avg # of iterations = 1.0 + + total cpu time spent up to now is 0.6 secs + + total energy = -15.84982619 Ry + Harris-Foulkes estimate = -15.87079416 Ry + estimated scf accuracy < 0.06161703 Ry + + iteration # 2 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 7.70E-04, avg # of iterations = 1.0 + + total cpu time spent up to now is 0.7 secs + + total energy = -15.85288351 Ry + Harris-Foulkes estimate = -15.85318795 Ry + estimated scf accuracy < 0.00216687 Ry + + iteration # 3 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 2.71E-05, avg # of iterations = 2.4 + + total cpu time spent up to now is 0.8 secs + + total energy = -15.85332918 Ry + Harris-Foulkes estimate = -15.85336185 Ry + estimated scf accuracy < 0.00007437 Ry + + iteration # 4 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 9.30E-07, avg # of iterations = 2.1 + + total cpu time spent up to now is 0.8 secs + + total energy = -15.85334986 Ry + Harris-Foulkes estimate = -15.85335396 Ry + estimated scf accuracy < 0.00000888 Ry + + iteration # 5 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.11E-07, avg # of iterations = 2.1 + + total cpu time spent up to now is 0.9 secs + + total energy = -15.85335134 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 0.00000011 Ry + + iteration # 6 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.35E-09, avg # of iterations = 2.6 + + total cpu time spent up to now is 1.0 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 2.9E-09 Ry + + iteration # 7 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 3.68E-11, avg # of iterations = 2.6 + + total cpu time spent up to now is 1.1 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 2.9E-11 Ry + + iteration # 8 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 3.65E-13, avg # of iterations = 3.3 + + total cpu time spent up to now is 1.2 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 5.4E-12 Ry + + iteration # 9 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.00E-13, avg # of iterations = 1.7 + + total cpu time spent up to now is 1.3 secs + + total energy = -15.85335138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 1.2E-13 Ry + + iteration # 10 ecut= 100.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.00E-13, avg # of iterations = 1.0 + + total cpu time spent up to now is 1.4 secs + + End of self-consistent calculation + + k = 0.0000 0.0000 0.0000 ( 4477 PWs) bands (ev): + + -5.8300 6.2061 6.2061 6.2061 + + k =-0.1250 0.1250-0.1250 ( 4507 PWs) bands (ev): + + -5.6230 4.6051 5.9132 5.9132 + + k =-0.2500 0.2500-0.2500 ( 4510 PWs) bands (ev): + + -5.0182 2.2559 5.4373 5.4373 + + k =-0.3750 0.3750-0.3750 ( 4501 PWs) bands (ev): + + -4.1058 0.2065 5.1074 5.1074 + + k = 0.5000-0.5000 0.5000 ( 4476 PWs) bands (ev): + + -3.4453 -0.8427 4.9947 4.9947 + + k = 0.0000 0.2500 0.0000 ( 4504 PWs) bands (ev): + + -5.5533 4.8935 5.3857 5.3857 + + k =-0.1250 0.3750-0.1250 ( 4517 PWs) bands (ev): + + -5.0777 2.9801 4.8669 4.9518 + + k =-0.2500 0.5000-0.2500 ( 4508 PWs) bands (ev): + + -4.2481 0.8896 4.3532 4.5964 + + k = 0.6250-0.3750 0.6250 ( 4486 PWs) bands (ev): + + -3.3613 -0.6068 3.9003 4.6231 + + k = 0.5000-0.2500 0.5000 ( 4491 PWs) bands (ev): + + -3.6148 -0.2257 3.7125 4.9256 + + k = 0.3750-0.1250 0.3750 ( 4497 PWs) bands (ev): + + -4.5602 1.5598 3.8591 5.4251 + + k = 0.2500 0.0000 0.2500 ( 4477 PWs) bands (ev): + + -5.2819 3.5267 4.5444 5.9125 + + k = 0.0000 0.5000 0.0000 ( 4520 PWs) bands (ev): + + -4.7329 2.7148 4.2862 4.2862 + + k =-0.1250 0.6250-0.1250 ( 4509 PWs) bands (ev): + + -4.0117 1.2745 3.4881 3.9636 + + k = 0.7500-0.2500 0.7500 ( 4482 PWs) bands (ev): + + -3.0647 -0.1975 2.6082 3.9678 + + k = 0.6250-0.1250 0.6250 ( 4477 PWs) bands (ev): + + -2.8512 -0.4657 2.1376 4.2926 + + k = 0.5000 0.0000 0.5000 ( 4489 PWs) bands (ev): + + -3.7521 0.7207 2.3750 4.8614 + + k = 0.0000 0.7500 0.0000 ( 4484 PWs) bands (ev): + + -3.4015 0.4708 3.5586 3.5586 + + k = 0.8750-0.1250 0.8750 ( 4479 PWs) bands (ev): + + -2.4888 -0.6253 2.7002 3.4815 + + k = 0.7500 0.0000 0.7500 ( 4454 PWs) bands (ev): + + -2.0305 -1.0339 1.8049 3.7440 + + k = 0.0000-1.0000 0.0000 ( 4456 PWs) bands (ev): + + -1.6267 -1.6267 3.3090 3.3090 + + k =-0.2500 0.5000 0.0000 ( 4503 PWs) bands (ev): + + -4.4807 1.9234 3.4393 4.7592 + + k = 0.6250-0.3750 0.8750 ( 4489 PWs) bands (ev): + + -3.5748 0.3447 2.8290 4.2439 + + k = 0.5000-0.2500 0.7500 ( 4486 PWs) bands (ev): + + -2.9014 -0.6278 2.7039 4.0076 + + k = 0.7500-0.2500 1.0000 ( 4484 PWs) bands (ev): + + -3.1970 0.2501 2.7770 3.3923 + + k = 0.6250-0.1250 0.8750 ( 4486 PWs) bands (ev): + + -2.3006 -0.7332 2.0576 3.1860 + + k = 0.5000 0.0000 0.7500 ( 4490 PWs) bands (ev): + + -2.6570 -0.3670 1.8851 3.5717 + + k =-0.2500-1.0000 0.0000 ( 4472 PWs) bands (ev): + + -1.5427 -1.5427 2.7194 2.7194 + + k =-0.5000-1.0000 0.0000 ( 4488 PWs) bands (ev): + + -1.4495 -1.4495 2.2655 2.2655 + + highest occupied level (ev): 6.2061 + +! total energy = -15.85435138 Ry + Harris-Foulkes estimate = -15.85335138 Ry + estimated scf accuracy < 4.0E-15 Ry + + The total energy is the sum of the following terms: + + one-electron contribution = 4.76680131 Ry + hartree contribution = 1.08149972 Ry + xc contribution = -4.81476914 Ry + ewald contribution = -16.88688327 Ry + + convergence has been achieved in 10 iterations + + Forces acting on atoms (cartesian axes, Ry/au): + + atom 1 type 1 force = 0.00000000 0.00000000 0.00000000 + atom 2 type 1 force = 0.00000000 0.00000000 -0.00000000 + + Total force = 0.000000 Total SCF correction = 0.000000 + + + Computing stress (Cartesian axis) and pressure + + total stress (Ry/bohr**3) (kbar) P= 0.05 + 0.00000032 -0.00000000 -0.00000000 0.05 -0.00 -0.00 + -0.00000000 0.00000032 0.00000000 -0.00 0.05 0.00 + -0.00000000 0.00000000 0.00000032 -0.00 0.00 0.05 + + + Writing output data file Si.save + + init_run : 0.06s CPU 0.23s WALL ( 1 calls) + electrons : 0.85s CPU 1.01s WALL ( 1 calls) + forces : 0.00s CPU 0.01s WALL ( 1 calls) + stress : 0.02s CPU 0.03s WALL ( 1 calls) + + Called by init_run: + wfcinit : 0.04s CPU 0.11s WALL ( 1 calls) + potinit : 0.00s CPU 0.01s WALL ( 1 calls) + + Called by electrons: + c_bands : 0.73s CPU 0.80s WALL ( 11 calls) + sum_band : 0.11s CPU 0.13s WALL ( 11 calls) + v_of_rho : 0.00s CPU 0.01s WALL ( 11 calls) + mix_rho : 0.00s CPU 0.01s WALL ( 11 calls) + + Called by c_bands: + init_us_2 : 0.01s CPU 0.03s WALL ( 725 calls) + cegterg : 0.69s CPU 0.74s WALL ( 319 calls) + + Called by sum_band: + + Called by *egterg: + h_psi : 0.62s CPU 0.65s WALL ( 980 calls) + g_psi : 0.00s CPU 0.00s WALL ( 632 calls) + cdiaghg : 0.05s CPU 0.10s WALL ( 922 calls) + + Called by h_psi: + h_psi:pot : 0.61s CPU 0.65s WALL ( 980 calls) + h_psi:calbec : 0.03s CPU 0.04s WALL ( 980 calls) + vloc_psi : 0.57s CPU 0.59s WALL ( 980 calls) + add_vuspsi : 0.01s CPU 0.01s WALL ( 980 calls) + + General routines + calbec : 0.03s CPU 0.05s WALL ( 1125 calls) + fft : 0.01s CPU 0.05s WALL ( 50 calls) + fftw : 0.57s CPU 0.64s WALL ( 8656 calls) + davcio : 0.00s CPU 0.06s WALL ( 29 calls) + + Parallel routines + fft_scatter : 0.29s CPU 0.31s WALL ( 8706 calls) + + PWSCF : 1.07s CPU 2.22s WALL + + + This run was terminated on: 19:30: 3 27Sep2017 + +=------------------------------------------------------------------------------= + JOB DONE. +=------------------------------------------------------------------------------= From 2ab45088289ead2cedbae7ad2d1307454da1b0a6 Mon Sep 17 00:00:00 2001 From: cpolanco Date: Thu, 8 Dec 2022 23:32:57 +0100 Subject: [PATCH 16/16] Added support to send the QE calculations to the cluster. For that created a class to handle cluster jobs. --- capolanco/RunConvergence.py | 41 +++++++++++-- .../__pycache__/ioclusterclass.cpython-39.pyc | Bin 0 -> 1384 bytes capolanco/ioclusterclass.py | 58 ++++++++++++++++++ capolanco/job.test.sh | 12 ++++ capolanco/job.test1.sh | 12 ++++ capolanco/job.test2.sh | 12 ++++ capolanco/job.test3.sh | 12 ++++ capolanco/job.test4.sh | 12 ++++ 8 files changed, 155 insertions(+), 4 deletions(-) create mode 100644 capolanco/__pycache__/ioclusterclass.cpython-39.pyc create mode 100644 capolanco/ioclusterclass.py create mode 100644 capolanco/job.test.sh create mode 100644 capolanco/job.test1.sh create mode 100644 capolanco/job.test2.sh create mode 100644 capolanco/job.test3.sh create mode 100644 capolanco/job.test4.sh diff --git a/capolanco/RunConvergence.py b/capolanco/RunConvergence.py index b78b0abd..892ecf6c 100644 --- a/capolanco/RunConvergence.py +++ b/capolanco/RunConvergence.py @@ -1,7 +1,8 @@ # This code will run a k-point convergence up to a desire delta energy - +import subprocess import ioqeclass as qe +import ioclusterclass as cluster ########################### ##### USER INPUTS @@ -21,11 +22,24 @@ ##### DEVELOPERS INPUTS ########################### +## Convergence # maximum of iterations Nitermax=20 # increasing step of kgrid kstep=2 +## Cluster +# number of nodes to be used +Nnodes=1 +# number of processors per node +ppn=8 +# queue +queue='OR' +# walltime +walltimehours=5 +walltimeminutes=3 + + ########################### ##### PROGRAM ########################### @@ -40,8 +54,23 @@ testin='test.scf.in' testout='test.scf.out' qeinput.save(filein,testin) +# Create the job to send to the cluster +# Initialize job class +job=cluster.jobclass() +# set up job class +job.name='test' +job.nodes=Nnodes +job.ppn=ppn +job.queue=queue +job.walltimehours=walltimehours +job.walltimeminutes=walltimeminutes +# create the job file +jobname=f'job.test.sh' +job.createjobQEpw(jobname,testin,testout) # Run initial test -##### pw.x test.scf.in test.scf.out +subprocess.run(['echo',f'runing {jobname}']) +##subprocess.run(['qsub',f'{jobname}']) + # Initialize pw.x output class qeoutput=qe.qepwoutput() # Read the Total energy from the output @@ -66,8 +95,12 @@ testout=f'test.scf{counter}.out' qeinput.save(filein,testin) - # Run initial test - ##### pw.x test.scf{counter}.in test.scf{counter}.out + # create the job file + jobname=f'job.test{counter}.sh' + job.createjobQEpw(jobname,testin,testout) + # Run QE calculation + subprocess.run(['echo',f'runing {jobname}']) + ##subprocess.run(['qsub',f'{jobname}']) # Read the Total energy from the output qeoutput.getenergy(testout) diff --git a/capolanco/__pycache__/ioclusterclass.cpython-39.pyc b/capolanco/__pycache__/ioclusterclass.cpython-39.pyc new file mode 100644 index 0000000000000000000000000000000000000000..12df40cf06d5a2fa7cc660073dcbf438be63afac GIT binary patch literal 1384 zcmZ`(&2Qv16t|OjCQWDh#V%SvLPoO^n!|P~K&#b?qQVv-K$>0lLrA%pGD8}C*?s5Mu;{Lf8dmO(&XV_z?UQE5&La~IN$*% zZ&6Hm52EyKcq)(5JTa#J^yNurXhYLfi=-5Wg3{1qscCs4KvkJi=oCZbZaCU)`3X#O z0KoAAF;wC|JnmgN+Fzjq?t_G^NO}z&G?smiU`u2glUIciZSTorfK zYa23_6U3lHMGw`h0N*{)q73{4KFerIY?{lVz}M!hu}(I>7cv*K6R zmDJ*SJsf>9Im(L3QDRP_s18TZzIj0(OhFgb8!eO5rb+heLB~V4?02STv|exJr&Nll z-tLULzS)ocz0deHeq58sdwY;$C*|}$q+w6l&rhHKc=-MEsJ=Usyvha5Wx}a2N(*CT zRNtGaOjiYcP^i{r`i!di?r-!O({W^p($K~>kV-)N&UFS?%bmRr9jrNUFNI!r;F`#i zG?zwzM_n`{zM#OzJ&k9wQaj539DuJ^2xasc}Hl6RVz0u(F)3<8=F^G%<)C+Nl zH~h$t@SU44!qkg!gztIv`^#4SkNb4ob4~8DGiD>k+5!MQVC<|)@*7Q`F)mZa^cG~& zA31Q>ZUx-lw0pAPDMZFWhyxPtG_tV|SG=03*V-u>(TZymsrk3?%QpX4?x8R)T1fr@ D1M5>| literal 0 HcmV?d00001 diff --git a/capolanco/ioclusterclass.py b/capolanco/ioclusterclass.py new file mode 100644 index 00000000..ea4e0716 --- /dev/null +++ b/capolanco/ioclusterclass.py @@ -0,0 +1,58 @@ +import numpy as np + + +## THINGS TO FIX + +class jobclass: + """This class creates jobs for the cluster""" + + ################### + ## Initialization function for the class + ################### + def __init__(self): + + ## name of the job + self.name='Unset' + ## number of nodes + self.nodes=np.int64(1) + ## number of processors per node + self.ppn=np.int64(1) + ## queue + self.queue='D' + ## walltime (in hours) + self.walltimehours=np.int64(1) + self.walltimeminutes=np.int64(0) + + + ################### + ## Create the job for QE pw.x calculation + ################### + def createjobQEpw(self,jobname,pwinput,pwoutput): + # Inputs + # jobname is the name of the job + # pwinput is the path of the input file + # pwoutput is the path of the output file + + print('') + print(f'#########################') + print(f'## Creating job {jobname}') + + # Open file + f=open(jobname,'w') + + # Write heather of job + f.write(f'#!/bin/bash\n\n') + f.write(f'#PBS -N {self.name}\n') + f.write(f'#PBS -l nodes={self.nodes}\n') + f.write(f'#PBS -l ppn={self.ppn}\n') + f.write(f'#PBS -q {self.queue}\n') + f.write(f'#PBS -j oe\n') + f.write(f'#PBS -l walltime={self.walltimehours:02d}:{self.walltimeminutes:02d}:00\n\n') + + f.write(f'cd $PBS_O_WORKDIR\n') + f.write(f'module load espresso\n') + f.write(f'mpirun -np $PBS_NP pw.x {pwinput} {pwoutput}\n') + + f.close() + + diff --git a/capolanco/job.test.sh b/capolanco/job.test.sh new file mode 100644 index 00000000..ddcc703e --- /dev/null +++ b/capolanco/job.test.sh @@ -0,0 +1,12 @@ +#!/bin/bash + +#PBS -N test +#PBS -l nodes=1 +#PBS -l ppn=8 +#PBS -q OR +#PBS -j oe +#PBS -l walltime=05:03:00 + +cd $PBS_O_WORKDIR +module load espresso +mpirun -np $PBS_NP pw.x test.scf.in test.scf.out diff --git a/capolanco/job.test1.sh b/capolanco/job.test1.sh new file mode 100644 index 00000000..9ce1cf81 --- /dev/null +++ b/capolanco/job.test1.sh @@ -0,0 +1,12 @@ +#!/bin/bash + +#PBS -N test +#PBS -l nodes=1 +#PBS -l ppn=8 +#PBS -q OR +#PBS -j oe +#PBS -l walltime=05:03:00 + +cd $PBS_O_WORKDIR +module load espresso +mpirun -np $PBS_NP pw.x test.scf1.in test.scf1.out diff --git a/capolanco/job.test2.sh b/capolanco/job.test2.sh new file mode 100644 index 00000000..1b628d2c --- /dev/null +++ b/capolanco/job.test2.sh @@ -0,0 +1,12 @@ +#!/bin/bash + +#PBS -N test +#PBS -l nodes=1 +#PBS -l ppn=8 +#PBS -q OR +#PBS -j oe +#PBS -l walltime=05:03:00 + +cd $PBS_O_WORKDIR +module load espresso +mpirun -np $PBS_NP pw.x test.scf2.in test.scf2.out diff --git a/capolanco/job.test3.sh b/capolanco/job.test3.sh new file mode 100644 index 00000000..33c390a3 --- /dev/null +++ b/capolanco/job.test3.sh @@ -0,0 +1,12 @@ +#!/bin/bash + +#PBS -N test +#PBS -l nodes=1 +#PBS -l ppn=8 +#PBS -q OR +#PBS -j oe +#PBS -l walltime=05:03:00 + +cd $PBS_O_WORKDIR +module load espresso +mpirun -np $PBS_NP pw.x test.scf3.in test.scf3.out diff --git a/capolanco/job.test4.sh b/capolanco/job.test4.sh new file mode 100644 index 00000000..26d9d500 --- /dev/null +++ b/capolanco/job.test4.sh @@ -0,0 +1,12 @@ +#!/bin/bash + +#PBS -N test +#PBS -l nodes=1 +#PBS -l ppn=8 +#PBS -q OR +#PBS -j oe +#PBS -l walltime=05:03:00 + +cd $PBS_O_WORKDIR +module load espresso +mpirun -np $PBS_NP pw.x test.scf4.in test.scf4.out