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@dimonaks
dimonaks committed Nov 3, 2016
1 parent 5f42481 commit 525f61e
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6 changes: 3 additions & 3 deletions analysis.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,8 @@ def calc_redox(cl1, cl2, energy_ref = None):
cl2 (Calculation) - structure with lower concentration
energy_ref (float) - energy in eV per one alkali ion in anode; default value is for Li; -1.31 eV for Na, -1.02 eV for K
"""
cl1 = cl1
cl2 = cl2
if cl1 is None or cl2 is None:
return

energy_ref_dict = {3:-1.9, 11:-1.31, 19:-1.02}
z_alk_ions = [3, 11, 19]
Expand Down Expand Up @@ -78,7 +78,7 @@ def calc_redox(cl1, cl2, energy_ref = None):
# final_outstring = ("{:} | {:.2f} eV \n1".format(cl1.id[0]+'.'+cl1.id[1], redox ))
final_outstring = ("{:30} | {:10.2f} eV | {:10.1f} %".format(cl1.name, redox, vol_red ))

printlog( final_outstring )
printlog( final_outstring, end = '\n' )

try:
results_dic = {'is':cl1.id[0], 'redox_pot':redox, 'id_is':cl1.id, 'id_ds':cl2.id,
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2 changes: 1 addition & 1 deletion database.py
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Original file line number Diff line number Diff line change
Expand Up @@ -252,7 +252,7 @@ def check(key, inquiry_keys):


if len(x1s) == 0 or len(x2s) == 0:
print('No information in database for this inquire')
print('No information in database for this inquire:', x1, x2, mat, str(inquiry_keys) )
return None, None

key1 = x1s[0]
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282 changes: 214 additions & 68 deletions tutorials/working_with_database.ipynb
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Original file line number Diff line number Diff line change
@@ -1,46 +1,81 @@
{
"metadata": {
"name": "",
"signature": "sha256:014b208250907b1d16d86d21c53f4bd29151965472dfbfbccda1bc64bde3816a"
"signature": "sha256:e1b4245844ccede90e9e49397e097a17e649aceb667830051a0f53fce50fc2a5"
},
"nbformat": 3,
"nbformat_minor": 0,
"worksheets": [
{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"###1. Install required packages:\n",
"\n",
"- Install [Anaconda](https://www.continuum.io/downloads). For linux it is enought to install just [IPython](https://ipython.org/install.html) or [Jupyter Notebook](https://jupyter.readthedocs.io/en/latest/install.html)\n",
"- Install [paramiko](http://www.paramiko.org/) package by running in command line *pip install paramiko*\n",
"- Download siman package from https://github.com/dimonaks/siman/archive/v0.2.zip \n",
" and unpack into your folder, for example *'C:/programms/siman-0.2'*\n",
"- Download SSHTools from http://zhugayevych.me/python/SSHTools/SSHTools.zip and unpack into *'C:/programms/SSHTools'*\n",
"- open this file (*siman-0.2/tutorials/working_with_database.ipynb*) in Notebook\n",
"\n",
"###2. Import packages:"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"for mat in ['LiFePO4', 'LiTiO2']:\n",
" # cl1, cl2 = get_from_database('x1', 'x0', mat, inquiry_keys = ['UGGA-Upaw400'])\n",
" cl1, cl2 = get_from_database('x1', 'x0', mat, inquiry_keys = [''], silent = True)\n",
" calc_redox(cl1, cl2)\n"
"import sys\n",
"sys.path.extend(['/home/aksenov/Simulation_wrapper/siman', '/home/aksenov/Simulation_wrapper/SSHTools'])\n",
"sys.path.extend(['C:/programms/siman-0.2', 'C:/programms/SSHTools']) #path to siman package and SSHtools\n",
"from analysis import calc_redox\n",
"from database import get_from_database\n",
"from SSHTools import SSHTools"
],
"language": "python",
"metadata": {},
"outputs": []
"outputs": [],
"prompt_number": 9
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"###3. Initialize ssh:\n",
"The database server address is '10.30.100.28'. Use your account data and private rsa key (created earlier and added to server)"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"import sys\n",
"sys.path.append('/home/aksenov/Simulation_wrapper') #path to siman package\n",
"sys.path.append('/home/aksenov/Simulation_wrapper/siman') #path to siman package\n",
"sys.path.append('/home/aksenov/Simulation_wrapper/SSHTools') #path to ssh tools\n",
"from siman.analysis import calc_redox\n",
"from siman.database import get_from_database\n",
"from SSHTools import SSHTools\n",
"\n",
"ssh = SSHTools()\n",
"\n",
"# ssh.setup(user=\"Andriy.Zhugayevych\",host=\"cluster.skoltech.ru\",pkey=\"C:/Users/azh/Sys/Internet/SSH/skoltech/key2.ppk\")\n",
"\n",
"ssh.setup(user=\"aksenov\",host=\"10.30.100.28\",pkey=\"/home/aksenov/.ssh/id_rsa\")\n",
"\n",
"cl1, cl2 = get_from_database('x1', 'x0', 'LiFePO4', inquiry_keys = ['UGGA'], ssh_object = ssh)\n",
"calc_redox(cl1, cl2)\n"
"ssh.setup(user=\"aksenov\",host=\"10.30.100.28\",pkey=\"/home/aksenov/.ssh/id_rsa\")"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 2
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"###4. Access to database\n",
"The first two arguments are concentrations. The second argument is material. \n",
"To clarify the inquiry use *inquiry_keys*. To switch off messages use *silent = 1*"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"cl1, cl2 = get_from_database('x1', 'x0', 'LiTiS2', ssh_object = ssh)\n",
"calc_redox(cl1, cl2)"
],
"language": "python",
"metadata": {},
Expand All @@ -51,69 +86,180 @@
"text": [
"\n",
"Files for x1 :\n",
"1 LiFePO4/bin/x1_UGGA-Upaw400.pickle\n",
"2 LiFePO4/bin/x1s_UGGA-Upaw400.pickle\n",
"3 LiFePO4/bin/x1_UGGA-Upaw400_111.pickle\n",
"4 LiFePO4/bin/x1_UGGA-Upaw400_122.pickle\n",
"5 LiFePO4/bin/x1_UGGA-Upaw400_122s.pickle\n",
"6 LiFePO4/bin/x1_UGGA-Upaw400_122m.pickle\n",
"7 LiFePO4/bin/x1_UGGA-Upaw400_111m.pickle\n",
"8 LiFePO4/bin/x1_UGGA-Upaw400_111s.pickle\n",
"9 LiFePO4/em/bin/x1_UGGA-Upaw400_vs5.pickle\n",
"10 LiFePO4/em/bin/x1_UGGA-Upaw400_vs3.pickle\n",
"11 LiFePO4/em/bin/x1_UGGA-Upaw400_vs1.pickle\n",
"12 LiFePO4/em/bin/x1_UGGA-Upaw400_vs2.pickle\n",
"13 LiFePO4/em/bin/x1_UGGA-Upaw400_vs4.pickle\n",
"14 LiFePO4/em/bin/x1_UGGA-Upaw400_cg4.pickle\n",
"15 LiFePO4/em/bin/x1s_UGGA-Upaw400_cg2.pickle\n",
"16 LiFePO4/em/bin/x1_UGGA-Upaw400_111s_cg2.pickle\n",
"17 LiFePO4/em/bin/x1_UGGA-Upaw400_122s_cg2.pickle\n",
"18 LiFePO4/em/bin/x1_UGGA-Upaw400_111m_cg2.pickle\n",
"19 LiFePO4/em/bin/x1_UGGA-Upaw400_122m_cg2.pickle\n",
"20 LiFePO4/bin/x1_UGGA-Upaw400_UHSE06paw400.pickle\n",
"21 LiFePO4/bin/x1_UGGA-Upaw400_UGGA-Upaw600.pickle\n",
"1 LiTiS2/bin/x1_PBEpaw400.pickle\n",
"2 LiTiS2/bin/x1_UGGA-Upaw400.pickle\n",
"3 LiTiS2/em/bin/x1_PBEpaw400_cg4.pickle\n",
"4 LiTiS2/em/bin/x1_PBEpaw400_vs3.pickle\n",
"5 LiTiS2/em/bin/x1_PBEpaw400_vs5.pickle\n",
"6 LiTiS2/em/bin/x1_PBEpaw400_vs1.pickle\n",
"7 LiTiS2/em/bin/x1_PBEpaw400_vs2.pickle\n",
"8 LiTiS2/em/bin/x1_PBEpaw400_vs4.pickle\n",
"9 LiTiS2/em/bin/x1_UGGA-Upaw400_cg4.pickle\n",
"10 LiTiS2/em/bin/x1_UGGA-Upaw400_vs1.pickle\n",
"11 LiTiS2/em/bin/x1_UGGA-Upaw400_vs5.pickle\n",
"12 LiTiS2/em/bin/x1_UGGA-Upaw400_vs2.pickle\n",
"13 LiTiS2/em/bin/x1_UGGA-Upaw400_vs6.pickle\n",
"14 LiTiS2/em/bin/x1_UGGA-Upaw400_vs7.pickle\n",
"15 LiTiS2/em/bin/x1_UGGA-Upaw400_vs3.pickle\n",
"16 LiTiS2/em/bin/x1_UGGA-Upaw400_vs4.pickle\n",
"17 LiTiS2/aks/bin/x1_UPBE-Upaw400_s10_su_4uis_100.pickle\n",
"\n",
"Files for x0 :\n",
"1 LiFePO4/bin/x0_UGGA-Upaw400.pickle\n",
"2 LiFePO4/bin/x0_UGGA-Upaw400_122.pickle\n",
"3 LiFePO4/bin/x0_UGGA-Upaw400_234.pickle\n",
"4 LiFePO4/bin/x0_UGGA-Upaw400_111.pickle\n",
"5 LiFePO4/bin/x0_UGGA-Upaw400_122m.pickle\n",
"6 LiFePO4/bin/x0_UGGA-Upaw400_111s.pickle\n",
"7 LiFePO4/bin/x0_UGGA-Upaw400_111m.pickle\n",
"8 LiFePO4/bin/x0_UGGA-Upaw400_122s.pickle\n",
"9 LiFePO4/em/bin/x0_UGGA-Upaw400_vs4.pickle\n",
"10 LiFePO4/em/bin/x0_UGGA-Upaw400_cg4.pickle\n",
"11 LiFePO4/em/bin/x0_UGGA-Upaw400_vs3.pickle\n",
"12 LiFePO4/em/bin/x0_UGGA-Upaw400_vs2.pickle\n",
"13 LiFePO4/em/bin/x0_UGGA-Upaw400_vs6.pickle\n",
"14 LiFePO4/em/bin/x0_UGGA-Upaw400_vs1.pickle\n",
"15 LiFePO4/em/bin/x0_UGGA-Upaw400_vs5.pickle\n",
"16 LiFePO4/bin/x0_UGGA-Upaw400_122s_mchg.pickle\n",
"17 LiFePO4/em/bin/x0_UGGA-Upaw400_111m_cg2.pickle\n",
"18 LiFePO4/em/bin/x0_UGGA-Upaw400_122s_cg2.pickle\n",
"19 LiFePO4/em/bin/x0_UGGA-Upaw400_111s_cg2.pickle\n",
"20 LiFePO4/em/bin/x0_UGGA-Upaw400_122m_cg2.pickle\n",
"21 LiFePO4/bin/x0_UGGA-Upaw400_UGGA-Upaw600.pickle\n",
"22 LiFePO4/em/bin/x0_UGGA-Upaw400_234m_cg2gp.pickle\n",
"23 LiFePO4/em/bin/x0_UGGA-Upaw400_234s_cg2gp.pickle\n",
"1 LiTiS2/bin/x0_PBEpaw400.pickle\n",
"2 LiTiS2/em/bin/x0_PBEpaw400_vs1.pickle\n",
"3 LiTiS2/em/bin/x0_PBEpaw400_vs9.pickle\n",
"4 LiTiS2/em/bin/x0_PBEpaw400_vs3.pickle\n",
"5 LiTiS2/em/bin/x0_PBEpaw400_vs8.pickle\n",
"6 LiTiS2/em/bin/x0_PBEpaw400_vs2.pickle\n",
"7 LiTiS2/em/bin/x0_PBEpaw400_vs7.pickle\n",
"8 LiTiS2/em/bin/x0_PBEpaw400_vs4.pickle\n",
"9 LiTiS2/em/bin/x0_PBEpaw400_vs6.pickle\n",
"10 LiTiS2/em/bin/x0_PBEpaw400_vs5.pickle\n",
"11 LiTiS2/aks/bin/x0_UPBE-Upaw400_id_su_s10_su_4uis_100.pickle\n",
"\n",
"I choose first entries for both concentrations: LiTiS2/bin/x1_PBEpaw400.pickle and LiTiS2/bin/x0_PBEpaw400.pickle \n",
"\n",
"I choose first entries for both concentrations: LiFePO4/bin/x1_UGGA-Upaw400.pickle and LiFePO4/bin/x0_UGGA-Upaw400.pickle \n",
" Directory /tmp/LiTiS2/bin was created\n",
" \n",
"\n",
"-- LiFePO4 | 3.51 eV | 4.3 % \n",
"-- LiTiS2 | 1.91 eV | -2.7 % \n",
"\n"
]
},
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 15,
"prompt_number": 7,
"text": [
"{}"
]
}
],
"prompt_number": 15
"prompt_number": 7
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"#clarifying with 'UGGA' and 'vs2' tags\n",
"cl1, cl2 = get_from_database('x1', 'x0', 'LiTiS2', inquiry_keys = ['PBEpaw400', 'vs2'], ssh_object = ssh)\n",
"calc_redox(cl1, cl2)"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"Files for x1 :\n",
"1 LiTiS2/em/bin/x1_PBEpaw400_vs2.pickle\n",
"\n",
"Files for x0 :\n",
"1 LiTiS2/em/bin/x0_PBEpaw400_vs2.pickle\n",
"\n",
"I choose first entries for both concentrations: LiTiS2/em/bin/x1_PBEpaw400_vs2.pickle and LiTiS2/em/bin/x0_PBEpaw400_vs2.pickle \n",
"\n",
"-- LiTiS2 | 1.91 eV | 3.6 % \n"
]
},
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 4,
"text": [
"{}"
]
}
],
"prompt_number": 4
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"for mat in ['LiCoO2', 'LiMn2O4', 'LiFePO4', 'NaFePO4', 'NaMnAsO4', 'LiVPO4F',\n",
" 'KVPO4F', 'Na2FePO4F', 'KFeSO4F', 'LiVP2O7', 'Na2FeVF7']:\n",
" cl1, cl2 = get_from_database('x1', 'x0', mat, inquiry_keys = ['UGGA'], silent = 1, ssh_object = ssh)\n",
" calc_redox(cl1, cl2)"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"-- LiCoO2 | 3.93 eV | -0.1 % \n",
"-- LiMn2O4 | 3.63 eV | 5.7 % \n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"-- LiFePO4 | 3.51 eV | 4.3 % \n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"-- NaFePO4 | 3.09 eV | 12.5 % \n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"-- NaMnAsO4 | 3.53 eV | 13.9 % \n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"-- LiVPO4F | 3.93 eV | 7.3 % \n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"-- KVPO4F | 4.03 eV | 8.7 % \n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"-- Na2FePO4F | 4.11 eV | 3.9 % \n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"-- KFeSO4F | 3.79 eV | 10.5 % \n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"-- LiVP2O7 | 3.93 eV | 3.5 % \n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"-- Na2FeVF7 | 4.22 eV | 7.6 % \n"
]
}
],
"prompt_number": 8
}
],
"metadata": {}
Expand Down

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