log

Launch at 2019-06-27 18:10:19.705777
 

-- There is no dictionary of convergence lists. I create new 

-- There is no dictionary of inputsets. I create new 

-- There is still no history in database. The list is in header module  

-- There is no struct_des in database. The dict is in header module  


Launch at 2019-06-27 18:10:44.364918
 

-- There is no dictionary of convergence lists. I create new 

-- There is no dictionary of inputsets. I create new 

-- There is still no history in database. The list is in header module  

-- There is no struct_des in database. The dict is in header module  


Launch at 2019-06-27 18:14:01.862457
 

-- There is no dictionary of convergence lists. I create new 

-- There is no dictionary of inputsets. I create new 

-- There is still no history in database. The list is in header module  

-- There is no struct_des in database. The dict is in header module  


Launch at 2019-06-27 18:14:09.498863
 

-- There is no dictionary of convergence lists. I create new 

-- There is no dictionary of inputsets. I create new 

-- There is still no history in database. The list is in header module  

-- There is no struct_des in database. The dict is in header module  


Launch at 2019-06-27 18:17:14.993564
 

-- There is no dictionary of convergence lists. I create new 

-- There is no dictionary of inputsets. I create new 

-- There is still no history in database. The list is in header module  

-- There is no struct_des in database. The dict is in header module  


Launch at 2019-06-27 18:17:17.544968
 

-- There is no dictionary of convergence lists. I create new 

-- There is no dictionary of inputsets. I create new 

-- There is still no history in database. The list is in header module  

-- There is no struct_des in database. The dict is in header module  


Launch at 2019-06-27 18:17:19.729706
 

-- There is no dictionary of convergence lists. I create new 

-- There is no dictionary of inputsets. I create new 

-- There is still no history in database. The list is in header module  

-- There is no struct_des in database. The dict is in header module  


Launch at 2019-06-27 18:17:21.255982
 

-- There is no dictionary of convergence lists. I create new 

-- There is no dictionary of inputsets. I create new 

-- There is still no history in database. The list is in header module  

-- There is no struct_des in database. The dict is in header module  


Launch at 2019-06-27 18:17:22.958494
 

-- There is no dictionary of convergence lists. I create new 

-- There is no dictionary of inputsets. I create new 

-- There is still no history in database. The list is in header module  

-- There is no struct_des in database. The dict is in header module  


Launch at 2019-06-27 18:17:44.303841
 

-- There is no dictionary of convergence lists. I create new 

-- There is no dictionary of inputsets. I create new 

-- There is still no history in database. The list is in header module  

-- There is no struct_des in database. The dict is in header module  


Launch at 2019-06-27 18:18:16.286864
 

-- There is no dictionary of convergence lists. I create new 

-- There is no dictionary of inputsets. I create new 

-- There is still no history in database. The list is in header module  

-- There is no struct_des in database. The dict is in header module  


Launch at 2019-06-27 18:18:26.748053
 

-- There is no dictionary of convergence lists. I create new 

-- There is no dictionary of inputsets. I create new 

-- There is still no history in database. The list is in header module  

-- There is no struct_des in database. The dict is in header module  


Launch at 2019-06-27 18:18:29.244087
 

-- There is no dictionary of convergence lists. I create new 

-- There is no dictionary of inputsets. I create new 

-- There is still no history in database. The list is in header module  

-- There is no struct_des in database. The dict is in header module  


Launch at 2019-06-27 18:18:30.867780
 

-- There is no dictionary of convergence lists. I create new 

-- There is no dictionary of inputsets. I create new 

-- There is still no history in database. The list is in header module  

-- There is no struct_des in database. The dict is in header module  


Launch at 2019-06-27 18:18:32.774098
 

-- There is no dictionary of convergence lists. I create new 

-- There is no dictionary of inputsets. I create new 

-- There is still no history in database. The list is in header module  

-- There is no struct_des in database. The dict is in header module  


Launch at 2019-06-27 18:18:34.866393
 

-- There is no dictionary of convergence lists. I create new 

-- There is no dictionary of inputsets. I create new 

-- There is still no history in database. The list is in header module  

-- There is no struct_des in database. The dict is in header module  


Launch at 2019-06-27 18:18:36.213022
 

-- There is no dictionary of convergence lists. I create new 

-- There is no dictionary of inputsets. I create new 

-- There is still no history in database. The list is in header module  

-- There is no struct_des in database. The dict is in header module  


Launch at 2019-06-27 18:18:37.598377
 

-- There is no dictionary of convergence lists. I create new 

-- There is no dictionary of inputsets. I create new 

-- There is still no history in database. The list is in header module  

-- There is no struct_des in database. The dict is in header module  


Launch at 2019-06-27 18:18:43.505883
 

-- There is no dictionary of convergence lists. I create new 

-- There is no dictionary of inputsets. I create new 

-- There is still no history in database. The list is in header module  

-- There is no struct_des in database. The dict is in header module  


Launch at 2019-06-27 18:29:19.150012
 

-- There is no dictionary of convergence lists. I create new 

-- There is no dictionary of inputsets. I create new 

-- There is still no history in database. The list is in header module  

-- There is no struct_des in database. The dict is in header module  

-- You provided the following geo file explicitly  Li.POSCAR ; Version of file does not matter, I use *curver*= 1 as a new version 

-- vasp  format is detected 


Launch at 2019-06-27 18:32:25.705297
 

-- There is no dictionary of convergence lists. I create new 

-- There is no dictionary of inputsets. I create new 

-- There is still no history in database. The list is in header module  

-- There is no struct_des in database. The dict is in header module  

-- You provided the following geo file explicitly  Li.POSCAR ; Version of file does not matter, I use *curver*= 1 as a new version 

-- vasp  format is detected 

-- You provided the following geo file explicitly  Li.POSCAR ; Version of file does not matter, I use *curver*= 1 as a new version 

-- vasp  format is detected 

-- Vasp4 detected 

I take elements from the first line, The line is ['i2a=[Li] ; Li2.static.1'] you could use ! to add comment after name+
 

-- i2a list detected 

The following Z were read = [3]
 

VASP POSCAR format Li.POSCAR  was read
 

-- Attention!, cluster None is not found, using default cee 

-- You provided the following geo file explicitly  Li.POSCAR ; Version of file does not matter, I use *curver*= 1 as a new version 

-- vasp  format is detected 

-- Vasp4 detected 

I take elements from the first line, The line is ['i2a=[Li] ; Li2.static.1'] you could use ! to add comment after name+
 

-- i2a list detected 

The following Z were read = [3]
 

VASP POSCAR format Li.POSCAR  was read
 

-- We use sd cluster 

-- Running pwd on server ... 

-- /home/aksenov 

-- The home folder on cluster is  /home/aksenov 

-- add_loop: starting add_loop_inherit ... 

New structure name Li added to struct_des dict
 

There is no calculation with id ('Li', 'static', 1). I create new with set static
 

-- Running mkdir -p Li//Li.static/ on server ... 

--  

-- check_kpoints(): k-points are determined from kspacing 0.235 

-- check_kpoints(): I added  [9, 9, 9] as a k-grid for 0.235 in struct_des of Li 

-- check_kpoints(): Kpoint   mesh is:  [9, 9, 9] 

-- check_kpoints(): The actual k-spacings are  [ 0.23  0.23  0.23] 

-- remove_atoms(): Atoms ['void'] were removed 

-- Starting writing POSCAR Li//Li.static/1.POSCAR Vasp5: True 

-- POSCAR was written to /hdd/home/aksenov/Simulation_wrapper/siman/tutorials/test/Li//Li.static/1.POSCAR 

-- The value of savefile is oc 

-- Potentials from  /hdd/home/aksenov/scientific_projects/PAW_PBE_VASP are taken 

-- You provided the following geo file explicitly  Li.POSCAR ; Version of file does not matter, I use *curver*= 1 as a new version 

-- vasp  format is detected 

-- Vasp4 detected 

I take elements from the first line, The line is ['i2a=[Li] ; Li2.static.1'] you could use ! to add comment after name+
 

-- i2a list detected 

The following Z were read = [3]
 

VASP POSCAR format Li.POSCAR  was read
 

-- We use sd cluster 

-- Running pwd on server ... 

-- /home/aksenov 

-- The home folder on cluster is  /home/aksenov 

-- add_loop: starting add_loop_inherit ... 

-- add_calculation(): Li.static.1  has been already created and has state:  0.Initialized 

-- You asked to update existing calculation with id ('Li', 'static', 1); results are overwritten 

-- check_kpoints(): k-points will be used from *ngkpt_dict* of Li [9, 9, 9] 

-- check_kpoints(): Kpoint   mesh is:  [9, 9, 9] 

-- check_kpoints(): The actual k-spacings are  [ 0.23  0.23  0.23] 

-- remove_atoms(): Atoms ['void'] were removed 

-- Starting writing POSCAR Li//Li.static/1.POSCAR Vasp5: True 

-- POSCAR was written to /hdd/home/aksenov/Simulation_wrapper/siman/tutorials/test/Li//Li.static/1.POSCAR 

-- The value of savefile is oc 

-- Potentials from  /hdd/home/aksenov/scientific_projects/PAW_PBE_VASP are taken 

-- POTCAR files: ['/hdd/home/aksenov/scientific_projects/PAW_PBE_VASP/Li/POTCAR'] 

-- remove_atoms(): Atoms ['void'] were removed 

-- I found that at least 1  bands are required. I will use 1 bands; add_nbands =  1.25 

Li//Li.static/INCAR was generated
 

You said to generate KPOINTS file.
 

-- Attention! ngkpt =  [9, 9, 9]  is adopted from struct_des which you provided for it  Li  and kspacing =  0.235 

KPOINTS was generated
 

-- Files to copy: ['Li//Li.static/INCAR', 'Li//Li.static/KPOINTS', 'Li//Li.static/Li.static.run', 'Li//Li.static/POTCAR', 'Li//Li.static/1.POSCAR'] 

-- Running  mkdir -p /home/aksenov//Li//Li.static/ on server ... 

--  

-- push_to_server():  mkdir -p /home/aksenov//Li//Li.static/  

-- push_to_server(): uploading files  ['Li//Li.static/INCAR', 'Li//Li.static/KPOINTS', 'Li//Li.static/Li.static.run', 'Li//Li.static/POTCAR', 'Li//Li.static/1.POSCAR'] to sd /home/aksenov//Li//Li.static/ 

--  

-- Setting executable rights for batch script on server /home/aksenov//Li//Li.static/Li.static.run 

-- Running chmod +x /home/aksenov//Li//Li.static/Li.static.run on server ... 

--  


Run file created
 


Calculation ('Li', 'static', 1) successfully created

 

-- You provided the following geo file explicitly  Li.POSCAR ; Version of file does not matter, I use *curver*= 1 as a new version 

-- vasp  format is detected 

-- Vasp4 detected 

I take elements from the first line, The line is ['i2a=[Li] ; Li2.static.1'] you could use ! to add comment after name+
 

-- i2a list detected 

The following Z were read = [3]
 

VASP POSCAR format Li.POSCAR  was read
 

-- We use sd cluster 

-- Running pwd on server ... 

-- /home/aksenov 

-- The home folder on cluster is  /home/aksenov 

-- add_loop: starting add_loop_inherit ... 

-- add_calculation(): Li.static.1  has been already created and has state:  2. Ready for start 

-- check_kpoints(): k-points will be used from *ngkpt_dict* of Li [9, 9, 9] 

-- check_kpoints(): Kpoint   mesh is:  [9, 9, 9] 

-- check_kpoints(): The actual k-spacings are  [ 0.23  0.23  0.23] 

-- remove_atoms(): Atoms ['void'] were removed 

-- Starting writing POSCAR Li//Li.static/1.POSCAR Vasp5: True 

-- POSCAR was written to /hdd/home/aksenov/Simulation_wrapper/siman/tutorials/test/Li//Li.static/1.POSCAR 

-- The value of savefile is oc 

-- Potentials from  /hdd/home/aksenov/scientific_projects/PAW_PBE_VASP are taken 

-- POTCAR files: ['/hdd/home/aksenov/scientific_projects/PAW_PBE_VASP/Li/POTCAR'] 

-- remove_atoms(): Atoms ['void'] were removed 

-- I found that at least 1  bands are required. I will use 1 bands; add_nbands =  1.25 

Li//Li.static/INCAR was generated
 

You said to generate KPOINTS file.
 

-- Attention! ngkpt =  [9, 9, 9]  is adopted from struct_des which you provided for it  Li  and kspacing =  0.235 

KPOINTS was generated
 

-- Files to copy: ['Li//Li.static/INCAR', 'Li//Li.static/KPOINTS', 'Li//Li.static/Li.static.run', 'Li//Li.static/POTCAR', 'Li//Li.static/1.POSCAR'] 

-- Running  mkdir -p /home/aksenov/./Li//Li.static/ on server ... 

--  

-- push_to_server():  mkdir -p /home/aksenov/./Li//Li.static/  

-- push_to_server(): uploading files  ['Li//Li.static/INCAR', 'Li//Li.static/KPOINTS', 'Li//Li.static/Li.static.run', 'Li//Li.static/POTCAR', 'Li//Li.static/1.POSCAR'] to sd /home/aksenov/./Li//Li.static/ 

--  

-- Setting executable rights for batch script on server /home/aksenov/./Li//Li.static/Li.static.run 

-- Running chmod +x /home/aksenov/./Li//Li.static/Li.static.run on server ... 

--  


Run file created
 


Calculation ('Li', 'static', 1) successfully created

 

-- You provided the following geo file explicitly  Li.POSCAR ; Version of file does not matter, I use *curver*= 1 as a new version 

-- vasp  format is detected 

-- Vasp4 detected 

I take elements from the first line, The line is ['i2a=[Li] ; Li2.static.1'] you could use ! to add comment after name+
 

-- i2a list detected 

The following Z were read = [3]
 

VASP POSCAR format Li.POSCAR  was read
 

-- We use sd cluster 

-- Running pwd on server ... 

-- /home/aksenov 

-- The home folder on cluster is  /home/aksenov 

-- add_loop: starting add_loop_inherit ... 

-- add_calculation(): Li.static.1  has been already created and has state:  2. Ready for start 

-- check_kpoints(): k-points will be used from *ngkpt_dict* of Li [9, 9, 9] 

-- check_kpoints(): Kpoint   mesh is:  [9, 9, 9] 

-- check_kpoints(): The actual k-spacings are  [ 0.23  0.23  0.23] 

-- remove_atoms(): Atoms ['void'] were removed 

-- Starting writing POSCAR Li//Li.static/1.POSCAR Vasp5: True 

-- POSCAR was written to /hdd/home/aksenov/Simulation_wrapper/siman/tutorials/test/Li//Li.static/1.POSCAR 

-- The value of savefile is oc 

-- Potentials from  /hdd/home/aksenov/scientific_projects/PAW_PBE_VASP are taken 

-- POTCAR files: ['/hdd/home/aksenov/scientific_projects/PAW_PBE_VASP/Li/POTCAR'] 

-- remove_atoms(): Atoms ['void'] were removed 

-- I found that at least 1  bands are required. I will use 1 bands; add_nbands =  1.25 

Li//Li.static/INCAR was generated
 

You said to generate KPOINTS file.
 

-- Attention! ngkpt =  [9, 9, 9]  is adopted from struct_des which you provided for it  Li  and kspacing =  0.235 

KPOINTS was generated
 

-- Files to copy: ['Li//Li.static/INCAR', 'Li//Li.static/KPOINTS', 'Li//Li.static/Li.static.run', 'Li//Li.static/POTCAR', 'Li//Li.static/1.POSCAR'] 

-- Running  mkdir -p /home/aksenov/./Li//Li.static/ on server ... 

--  

-- push_to_server():  mkdir -p /home/aksenov/./Li//Li.static/  

-- push_to_server(): uploading files  ['Li//Li.static/INCAR', 'Li//Li.static/KPOINTS', 'Li//Li.static/Li.static.run', 'Li//Li.static/POTCAR', 'Li//Li.static/1.POSCAR'] to sd /home/aksenov/./Li//Li.static/ 

--  

-- Setting executable rights for batch script on server /home/aksenov/./Li//Li.static/Li.static.run 

-- Running chmod +x /home/aksenov/./Li//Li.static/Li.static.run on server ... 

--  


Run file created
 


Calculation ('Li', 'static', 1) successfully created

 


Launch at 2019-06-27 18:37:52.331772
 

-- There is no dictionary of convergence lists. I create new 

-- There is no dictionary of inputsets. I create new 

-- There is still no history in database. The list is in header module  

-- There is no struct_des in database. The dict is in header module  

-- You provided the following geo file explicitly  Li.POSCAR ; Version of file does not matter, I use *curver*= 1 as a new version 

-- vasp  format is detected 

-- Vasp4 detected 

I take elements from the first line, The line is ['i2a=[Li] ; Li2.static.1'] you could use ! to add comment after name+
 

-- i2a list detected 

The following Z were read = [3]
 

VASP POSCAR format Li.POSCAR  was read
 

-- We use sd cluster 

-- Running pwd on server ... 

-- /home/aksenov 

-- The home folder on cluster is  /home/aksenov 

-- add_loop: starting add_loop_inherit ... 

-- add_calculation(): Li.static.1  has been already created and has state:  2. Ready for start 

-- check_kpoints(): k-points will be used from *ngkpt_dict* of Li [9, 9, 9] 

-- check_kpoints(): Kpoint   mesh is:  [9, 9, 9] 

-- check_kpoints(): The actual k-spacings are  [ 0.23  0.23  0.23] 

-- remove_atoms(): Atoms ['void'] were removed 

-- Starting writing POSCAR Li//Li.static/1.POSCAR Vasp5: True 

-- POSCAR was written to /hdd/home/aksenov/Simulation_wrapper/siman/tutorials/test/Li//Li.static/1.POSCAR 

-- The value of savefile is oc 

-- Potentials from  /hdd/home/aksenov/scientific_projects/PAW_PBE_VASP are taken 

-- POTCAR files: ['/hdd/home/aksenov/scientific_projects/PAW_PBE_VASP/Li/POTCAR'] 

-- remove_atoms(): Atoms ['void'] were removed 

-- I found that at least 1  bands are required. I will use 1 bands; add_nbands =  1.25 

Li//Li.static/INCAR was generated
 

You said to generate KPOINTS file.
 

-- Attention! ngkpt =  [9, 9, 9]  is adopted from struct_des which you provided for it  Li  and kspacing =  0.235 

KPOINTS was generated
 

-- Files to copy: ['Li//Li.static/INCAR', 'Li//Li.static/KPOINTS', 'Li//Li.static/Li.static.run', 'Li//Li.static/POTCAR', 'Li//Li.static/1.POSCAR'] 

-- Running  mkdir -p /home/aksenov/./Li//Li.static/ on server ... 

--  

-- push_to_server():  mkdir -p /home/aksenov/./Li//Li.static/  

-- push_to_server(): uploading files  ['Li//Li.static/INCAR', 'Li//Li.static/KPOINTS', 'Li//Li.static/Li.static.run', 'Li//Li.static/POTCAR', 'Li//Li.static/1.POSCAR'] to sd /home/aksenov/./Li//Li.static/ 

--  

-- Setting executable rights for batch script on server /home/aksenov/./Li//Li.static/Li.static.run 

-- Running chmod +x /home/aksenov/./Li//Li.static/Li.static.run on server ... 

--  


Run file created
 


Calculation ('Li', 'static', 1) successfully created

 

-- Running  mkdir -p /home/aksenov on server ... 

--  

-- push_to_server():  mkdir -p /home/aksenov  

-- push_to_server(): uploading files  ['run'] to sd /home/aksenov 

--  

-- Running chmod +x run on server ... 

--  

-- run sent 

-- You provided the following geo file explicitly  Li.POSCAR ; Version of file does not matter, I use *curver*= 1 as a new version 

-- vasp  format is detected 

-- Vasp4 detected 

I take elements from the first line, The line is ['i2a=[Li] ; Li2.static.1'] you could use ! to add comment after name+
 

-- i2a list detected 

The following Z were read = [3]
 

VASP POSCAR format Li.POSCAR  was read
 

-- We use sd cluster 

-- Running pwd on server ... 

-- /home/aksenov 

-- The home folder on cluster is  /home/aksenov 

-- add_loop: starting add_loop_inherit ... 

-- add_calculation(): Li.static.1  has been already created and has state:  2. Ready for start 

-- check_kpoints(): k-points will be used from *ngkpt_dict* of Li [9, 9, 9] 

-- check_kpoints(): Kpoint   mesh is:  [9, 9, 9] 

-- check_kpoints(): The actual k-spacings are  [ 0.23  0.23  0.23] 

-- remove_atoms(): Atoms ['void'] were removed 

-- Starting writing POSCAR Li//Li.static/1.POSCAR Vasp5: True 

-- POSCAR was written to /hdd/home/aksenov/Simulation_wrapper/siman/tutorials/test/Li//Li.static/1.POSCAR 

-- The value of savefile is oc 

-- Potentials from  /hdd/home/aksenov/scientific_projects/PAW_PBE_VASP are taken 

-- POTCAR files: ['/hdd/home/aksenov/scientific_projects/PAW_PBE_VASP/Li/POTCAR'] 

-- remove_atoms(): Atoms ['void'] were removed 

-- I found that at least 1  bands are required. I will use 1 bands; add_nbands =  1.25 

Li//Li.static/INCAR was generated
 

You said to generate KPOINTS file.
 

-- Attention! ngkpt =  [9, 9, 9]  is adopted from struct_des which you provided for it  Li  and kspacing =  0.235 

KPOINTS was generated
 

-- Files to copy: ['Li//Li.static/INCAR', 'Li//Li.static/KPOINTS', 'Li//Li.static/Li.static.run', 'Li//Li.static/POTCAR', 'Li//Li.static/1.POSCAR'] 

-- Running  mkdir -p /home/aksenov/./Li//Li.static/ on server ... 

--  

-- push_to_server():  mkdir -p /home/aksenov/./Li//Li.static/  

-- push_to_server(): uploading files  ['Li//Li.static/INCAR', 'Li//Li.static/KPOINTS', 'Li//Li.static/Li.static.run', 'Li//Li.static/POTCAR', 'Li//Li.static/1.POSCAR'] to sd /home/aksenov/./Li//Li.static/ 

--  

-- Setting executable rights for batch script on server /home/aksenov/./Li//Li.static/Li.static.run 

-- Running chmod +x /home/aksenov/./Li//Li.static/Li.static.run on server ... 

--  


Run file created
 


Calculation ('Li', 'static', 1) successfully created

 

-- Running  mkdir -p /home/aksenov on server ... 

--  

-- push_to_server():  mkdir -p /home/aksenov  

-- push_to_server(): uploading files  ['run'] to sd /home/aksenov 

--  

-- Running chmod +x run on server ... 

--  

-- run sent 

-- You provided the following geo file explicitly  Li.POSCAR ; Version of file does not matter, I use *curver*= 1 as a new version 

-- vasp  format is detected 

-- Vasp4 detected 

I take elements from the first line, The line is ['i2a=[Li] ; Li2.static.1'] you could use ! to add comment after name+
 

-- i2a list detected 

The following Z were read = [3]
 

VASP POSCAR format Li.POSCAR  was read
 

-- We use sd cluster 

-- Running pwd on server ... 

-- /home/aksenov 

-- The home folder on cluster is  /home/aksenov 

-- add_loop: starting add_loop_inherit ... 

-- add_calculation(): Li.static.1  has been already created and has state:  2. Ready for start 

-- check_kpoints(): k-points will be used from *ngkpt_dict* of Li [9, 9, 9] 

-- check_kpoints(): Kpoint   mesh is:  [9, 9, 9] 

-- check_kpoints(): The actual k-spacings are  [ 0.23  0.23  0.23] 

-- remove_atoms(): Atoms ['void'] were removed 

-- Starting writing POSCAR Li//Li.static/1.POSCAR Vasp5: True 

-- POSCAR was written to /hdd/home/aksenov/Simulation_wrapper/siman/tutorials/test/Li//Li.static/1.POSCAR 

-- The value of savefile is oc 

-- Potentials from  /hdd/home/aksenov/scientific_projects/PAW_PBE_VASP are taken 

-- POTCAR files: ['/hdd/home/aksenov/scientific_projects/PAW_PBE_VASP/Li/POTCAR'] 

-- remove_atoms(): Atoms ['void'] were removed 

-- I found that at least 1  bands are required. I will use 1 bands; add_nbands =  1.25 

Li//Li.static/INCAR was generated
 

You said to generate KPOINTS file.
 

-- Attention! ngkpt =  [9, 9, 9]  is adopted from struct_des which you provided for it  Li  and kspacing =  0.235 

KPOINTS was generated
 

-- Files to copy: ['Li//Li.static/INCAR', 'Li//Li.static/KPOINTS', 'Li//Li.static/Li.static.run', 'Li//Li.static/POTCAR', 'Li//Li.static/1.POSCAR'] 

-- Running  mkdir -p /home/aksenov/./Li//Li.static/ on server ... 

--  

-- push_to_server():  mkdir -p /home/aksenov/./Li//Li.static/  

-- push_to_server(): uploading files  ['Li//Li.static/INCAR', 'Li//Li.static/KPOINTS', 'Li//Li.static/Li.static.run', 'Li//Li.static/POTCAR', 'Li//Li.static/1.POSCAR'] to sd /home/aksenov/./Li//Li.static/ 

--  

-- Setting executable rights for batch script on server /home/aksenov/./Li//Li.static/Li.static.run 

-- Running chmod +x /home/aksenov/./Li//Li.static/Li.static.run on server ... 

--  


Run file created
 


Calculation ('Li', 'static', 1) successfully created

 

-- Running  mkdir -p /home/aksenov on server ... 

--  

-- push_to_server():  mkdir -p /home/aksenov  

-- push_to_server(): uploading files  ['run'] to sd /home/aksenov 

--  

-- Running chmod +x run on server ... 

--  

-- run sent 

-- Opening  only_calc.gdbm3 for writing 

-- saving key: ('Li', 'static', 1) 


End of work at 2019-06-27 18:38:44.470723
 


Launch at 2019-06-27 18:40:11.727651
 

-- You provided the following geo file explicitly  Li.POSCAR ; Version of file does not matter, I use *curver*= 1 as a new version 

-- vasp  format is detected 

-- Vasp4 detected 

I take elements from the first line, The line is ['i2a=[Li] ; Li2.static.1'] you could use ! to add comment after name+
 

-- i2a list detected 

The following Z were read = [3]
 

VASP POSCAR format Li.POSCAR  was read
 

-- We use sd cluster 

-- Running pwd on server ... 

-- /home/aksenov 

-- The home folder on cluster is  /home/aksenov 

-- add_loop: starting add_loop_inherit ... 

-- add_calculation(): Li.static.1  has been already created and has state:  2. Ready for start 

-- check_kpoints(): k-points will be used from *ngkpt_dict* of Li [9, 9, 9] 

-- check_kpoints(): Kpoint   mesh is:  [9, 9, 9] 

-- check_kpoints(): The actual k-spacings are  [ 0.23  0.23  0.23] 

-- remove_atoms(): Atoms ['void'] were removed 

-- Starting writing POSCAR Li//Li.static/1.POSCAR Vasp5: True 

-- POSCAR was written to /hdd/home/aksenov/Simulation_wrapper/siman/tutorials/test/Li//Li.static/1.POSCAR 

-- The value of savefile is oc 

-- Potentials from  /hdd/home/aksenov/scientific_projects/PAW_PBE_VASP are taken 

-- POTCAR files: ['/hdd/home/aksenov/scientific_projects/PAW_PBE_VASP/Li/POTCAR'] 

-- remove_atoms(): Atoms ['void'] were removed 

-- I found that at least 1  bands are required. I will use 1 bands; add_nbands =  1.25 

Li//Li.static/INCAR was generated
 

You said to generate KPOINTS file.
 

-- Attention! ngkpt =  [9, 9, 9]  is adopted from struct_des which you provided for it  Li  and kspacing =  0.235 

KPOINTS was generated
 

-- Files to copy: ['Li//Li.static/INCAR', 'Li//Li.static/KPOINTS', 'Li//Li.static/Li.static.run', 'Li//Li.static/POTCAR', 'Li//Li.static/1.POSCAR'] 

-- Running  mkdir -p /home/aksenov//Li//Li.static/ on server ... 

--  

-- push_to_server():  mkdir -p /home/aksenov//Li//Li.static/  

-- push_to_server(): uploading files  ['Li//Li.static/INCAR', 'Li//Li.static/KPOINTS', 'Li//Li.static/Li.static.run', 'Li//Li.static/POTCAR', 'Li//Li.static/1.POSCAR'] to sd /home/aksenov//Li//Li.static/ 

--  

-- Setting executable rights for batch script on server /home/aksenov//Li//Li.static/Li.static.run 

-- Running chmod +x /home/aksenov//Li//Li.static/Li.static.run on server ... 

--  


Run file created
 


Calculation ('Li', 'static', 1) successfully created

 

-- Opening  only_calc.gdbm3 for writing 

-- saving key: ('Li', 'static', 1) 


End of work at 2019-06-27 18:40:15.903603
 


Launch at 2019-06-27 18:42:14.890299
 

-- You provided the following geo file explicitly  Li.POSCAR ; Version of file does not matter, I use *curver*= 1 as a new version 

-- vasp  format is detected 

-- Vasp4 detected 

I take elements from the first line, The line is ['i2a=[Li] ; Li2.static.1'] you could use ! to add comment after name+
 

-- i2a list detected 

The following Z were read = [3]
 

VASP POSCAR format Li.POSCAR  was read
 

-- We use sd cluster 

-- Running pwd on server ... 

-- /home/aksenov 

-- The home folder on cluster is  /home/aksenov 

-- add_loop: starting add_loop_inherit ... 

-- add_calculation(): Li.static.1  has been already created and has state:  2. Ready for start 

-- check_kpoints(): k-points will be used from *ngkpt_dict* of Li [9, 9, 9] 

-- check_kpoints(): Kpoint   mesh is:  [9, 9, 9] 

-- check_kpoints(): The actual k-spacings are  [ 0.23  0.23  0.23] 

-- remove_atoms(): Atoms ['void'] were removed 

-- Starting writing POSCAR Li//Li.static/1.POSCAR Vasp5: True 

-- POSCAR was written to /hdd/home/aksenov/Simulation_wrapper/siman/tutorials/test/Li//Li.static/1.POSCAR 

-- The value of savefile is oc 

-- Potentials from  /hdd/home/aksenov/scientific_projects/PAW_PBE_VASP are taken 

-- POTCAR files: ['/hdd/home/aksenov/scientific_projects/PAW_PBE_VASP/Li/POTCAR'] 

-- remove_atoms(): Atoms ['void'] were removed 

-- I found that at least 1  bands are required. I will use 1 bands; add_nbands =  1.25 

Li//Li.static/INCAR was generated
 

You said to generate KPOINTS file.
 

-- Attention! ngkpt =  [9, 9, 9]  is adopted from struct_des which you provided for it  Li  and kspacing =  0.235 

KPOINTS was generated
 

-- Files to copy: ['Li//Li.static/INCAR', 'Li//Li.static/KPOINTS', 'Li//Li.static/Li.static.run', 'Li//Li.static/POTCAR', 'Li//Li.static/1.POSCAR'] 

-- Running  mkdir -p /home/aksenov//Li//Li.static/ on server ... 

--  

-- push_to_server():  mkdir -p /home/aksenov//Li//Li.static/  

-- push_to_server(): uploading files  ['Li//Li.static/INCAR', 'Li//Li.static/KPOINTS', 'Li//Li.static/Li.static.run', 'Li//Li.static/POTCAR', 'Li//Li.static/1.POSCAR'] to sd /home/aksenov//Li//Li.static/ 

--  

-- Setting executable rights for batch script on server /home/aksenov//Li//Li.static/Li.static.run 

-- Running chmod +x /home/aksenov//Li//Li.static/Li.static.run on server ... 

--  


Run file created
 


Calculation ('Li', 'static', 1) successfully created

 

-- Running  mkdir -p /home/aksenov on server ... 

--  

-- push_to_server():  mkdir -p /home/aksenov  

-- push_to_server(): uploading files  ['run'] to sd /home/aksenov 

--  

-- Running chmod +x run on server ... 

--  

-- run sent 

-- Running ./run on server ... 

-- ./run: line 3: Li.static.run: command not found 

-- ./run: line 3: Li.static.run: command not found 

-- To read results use  res_loop('Li', ['static'], [1], show = 'fo'  )     # , on 2019-06-27   ; possible options for show: fit, fo, fop, en, mag, magp, smag, maga, occ, occ1, mep, mepp 

-- Opening  only_calc.gdbm3 for writing 

-- saving key: ('Li', 'static', 1) 


End of work at 2019-06-27 18:42:19.465145
 


Launch at 2019-06-27 18:43:59.647237
 

-- You provided the following geo file explicitly  Li.POSCAR ; Version of file does not matter, I use *curver*= 1 as a new version 

-- vasp  format is detected 

-- Vasp4 detected 

I take elements from the first line, The line is ['i2a=[Li] ; Li2.static.1'] you could use ! to add comment after name+
 

-- i2a list detected 

The following Z were read = [3]
 

VASP POSCAR format Li.POSCAR  was read
 

-- We use sd cluster 

-- Running pwd on server ... 

-- /home/aksenov 

-- The home folder on cluster is  /home/aksenov 

-- add_loop: starting add_loop_inherit ... 

-- add_calculation(): Li.static.1  has been already created and has state:  2. Ready for start 

-- check_kpoints(): k-points will be used from *ngkpt_dict* of Li [9, 9, 9] 

-- check_kpoints(): Kpoint   mesh is:  [9, 9, 9] 

-- check_kpoints(): The actual k-spacings are  [ 0.23  0.23  0.23] 

-- remove_atoms(): Atoms ['void'] were removed 

-- Starting writing POSCAR Li//Li.static/1.POSCAR Vasp5: True 

-- POSCAR was written to /hdd/home/aksenov/Simulation_wrapper/siman/tutorials/test/Li//Li.static/1.POSCAR 

-- The value of savefile is oc 

-- Potentials from  /hdd/home/aksenov/scientific_projects/PAW_PBE_VASP are taken 

-- POTCAR files: ['/hdd/home/aksenov/scientific_projects/PAW_PBE_VASP/Li/POTCAR'] 

-- remove_atoms(): Atoms ['void'] were removed 

-- I found that at least 1  bands are required. I will use 1 bands; add_nbands =  1.25 

Li//Li.static/INCAR was generated
 

You said to generate KPOINTS file.
 

-- Attention! ngkpt =  [9, 9, 9]  is adopted from struct_des which you provided for it  Li  and kspacing =  0.235 

KPOINTS was generated
 

-- Files to copy: ['Li//Li.static/INCAR', 'Li//Li.static/KPOINTS', 'Li//Li.static/Li.static.run', 'Li//Li.static/POTCAR', 'Li//Li.static/1.POSCAR'] 

-- Running  mkdir -p /home/aksenov//Li//Li.static/ on server ... 

--  

-- push_to_server():  mkdir -p /home/aksenov//Li//Li.static/  

-- push_to_server(): uploading files  ['Li//Li.static/INCAR', 'Li//Li.static/KPOINTS', 'Li//Li.static/Li.static.run', 'Li//Li.static/POTCAR', 'Li//Li.static/1.POSCAR'] to sd /home/aksenov//Li//Li.static/ 

--  

-- Setting executable rights for batch script on server /home/aksenov//Li//Li.static/Li.static.run 

-- Running chmod +x /home/aksenov//Li//Li.static/Li.static.run on server ... 

--  


Run file created
 


Calculation ('Li', 'static', 1) successfully created

 

-- Running  mkdir -p /home/aksenov on server ... 

--  

-- push_to_server():  mkdir -p /home/aksenov  

-- push_to_server(): uploading files  ['run'] to sd /home/aksenov 

--  

-- Running chmod +x run on server ... 

--  

-- run sent 

-- Running ./run on server ... 

--------------------------------------------------------------------------
mpirun was unable to launch the specified application as it could not find an executable:

Executable: vasp
Node: Precision-T1700

while attempting to start process rank 0.
--------------------------------------------------------------------------
mv: cannot stat ‘OUTCAR’: No such file or directory
mv: cannot stat ‘CONTCAR’: No such file or directory
cp: cannot stat ‘CHGCAR’: No such file or directory
gzip: 1.CHGCAR: No such file or directory
rm: cannot remove ‘WAVECAR’: No such file or directory
rm: cannot remove ‘PROCAR’: No such file or directory
rm: cannot remove ‘DOSCAR’: No such file or directory
rm: cannot remove ‘OSZICAR’: No such file or directory
rm: cannot remove ‘PCDAT’: No such file or directory
rm: cannot remove ‘REPORT’: No such file or directory
rm: cannot remove ‘XDATCAR’: No such file or directory
rm: cannot remove ‘vasprun.xml’: No such file or directory
rm: cannot remove ‘RUNNING’: No such file or directory 

--------------------------------------------------------------------------
mpirun was unable to launch the specified application as it could not find an executable:

Executable: vasp
Node: Precision-T1700

while attempting to start process rank 0.
--------------------------------------------------------------------------
mv: cannot stat ‘OUTCAR’: No such file or directory
mv: cannot stat ‘CONTCAR’: No such file or directory
cp: cannot stat ‘CHGCAR’: No such file or directory
gzip: 1.CHGCAR: No such file or directory
rm: cannot remove ‘WAVECAR’: No such file or directory
rm: cannot remove ‘PROCAR’: No such file or directory
rm: cannot remove ‘DOSCAR’: No such file or directory
rm: cannot remove ‘OSZICAR’: No such file or directory
rm: cannot remove ‘PCDAT’: No such file or directory
rm: cannot remove ‘REPORT’: No such file or directory
rm: cannot remove ‘XDATCAR’: No such file or directory
rm: cannot remove ‘vasprun.xml’: No such file or directory
rm: cannot remove ‘RUNNING’: No such file or directory 

-- To read results use  res_loop('Li', ['static'], [1], show = 'fo'  )     # , on 2019-06-27   ; possible options for show: fit, fo, fop, en, mag, magp, smag, maga, occ, occ1, mep, mepp 

-- Opening  only_calc.gdbm3 for writing 

-- saving key: ('Li', 'static', 1) 


End of work at 2019-06-27 18:44:24.109754
 


Launch at 2019-06-27 18:45:49.475496
 

-- You provided the following geo file explicitly  Li.POSCAR ; Version of file does not matter, I use *curver*= 1 as a new version 

-- vasp  format is detected 

-- Vasp4 detected 

I take elements from the first line, The line is ['i2a=[Li] ; Li2.static.1'] you could use ! to add comment after name+
 

-- i2a list detected 

The following Z were read = [3]
 

VASP POSCAR format Li.POSCAR  was read
 

-- We use sd cluster 

-- Running pwd on server ... 

-- /home/aksenov 

-- The home folder on cluster is  /home/aksenov 

-- add_loop: starting add_loop_inherit ... 

-- add_calculation(): Li.static.1  has been already created and has state:  2. Ready for start 

-- check_kpoints(): k-points will be used from *ngkpt_dict* of Li [9, 9, 9] 

-- check_kpoints(): Kpoint   mesh is:  [9, 9, 9] 

-- check_kpoints(): The actual k-spacings are  [ 0.23  0.23  0.23] 

-- remove_atoms(): Atoms ['void'] were removed 

-- Starting writing POSCAR Li//Li.static/1.POSCAR Vasp5: True 

-- POSCAR was written to /hdd/home/aksenov/Simulation_wrapper/siman/tutorials/test/Li//Li.static/1.POSCAR 

-- The value of savefile is oc 

-- Potentials from  /hdd/home/aksenov/scientific_projects/PAW_PBE_VASP are taken 

-- POTCAR files: ['/hdd/home/aksenov/scientific_projects/PAW_PBE_VASP/Li/POTCAR'] 

-- remove_atoms(): Atoms ['void'] were removed 

-- I found that at least 1  bands are required. I will use 1 bands; add_nbands =  1.25 

Li//Li.static/INCAR was generated
 

You said to generate KPOINTS file.
 

-- Attention! ngkpt =  [9, 9, 9]  is adopted from struct_des which you provided for it  Li  and kspacing =  0.235 

KPOINTS was generated
 

-- Files to copy: ['Li//Li.static/INCAR', 'Li//Li.static/KPOINTS', 'Li//Li.static/Li.static.run', 'Li//Li.static/POTCAR', 'Li//Li.static/1.POSCAR'] 

-- Running  mkdir -p /home/aksenov//Li//Li.static/ on server ... 

--  

-- push_to_server():  mkdir -p /home/aksenov//Li//Li.static/  

-- push_to_server(): uploading files  ['Li//Li.static/INCAR', 'Li//Li.static/KPOINTS', 'Li//Li.static/Li.static.run', 'Li//Li.static/POTCAR', 'Li//Li.static/1.POSCAR'] to sd /home/aksenov//Li//Li.static/ 

--  

-- Setting executable rights for batch script on server /home/aksenov//Li//Li.static/Li.static.run 

-- Running chmod +x /home/aksenov//Li//Li.static/Li.static.run on server ... 

--  


Run file created
 


Calculation ('Li', 'static', 1) successfully created

 

-- Running  mkdir -p /home/aksenov on server ... 

--  

-- push_to_server():  mkdir -p /home/aksenov  

-- push_to_server(): uploading files  ['run'] to sd /home/aksenov 

--  

-- Running chmod +x run on server ... 

--  

-- run sent 

-- Running ./run on server ... 

./Li.static.run: line 4: vasp: command not found
mv: cannot stat ‘OUTCAR’: No such file or directory
mv: cannot stat ‘CONTCAR’: No such file or directory
cp: cannot stat ‘CHGCAR’: No such file or directory
gzip: 1.CHGCAR: No such file or directory
rm: cannot remove ‘WAVECAR’: No such file or directory
rm: cannot remove ‘PROCAR’: No such file or directory
rm: cannot remove ‘DOSCAR’: No such file or directory
rm: cannot remove ‘OSZICAR’: No such file or directory
rm: cannot remove ‘PCDAT’: No such file or directory
rm: cannot remove ‘REPORT’: No such file or directory
rm: cannot remove ‘XDATCAR’: No such file or directory
rm: cannot remove ‘vasprun.xml’: No such file or directory
rm: cannot remove ‘RUNNING’: No such file or directory 

./Li.static.run: line 4: vasp: command not found
mv: cannot stat ‘OUTCAR’: No such file or directory
mv: cannot stat ‘CONTCAR’: No such file or directory
cp: cannot stat ‘CHGCAR’: No such file or directory
gzip: 1.CHGCAR: No such file or directory
rm: cannot remove ‘WAVECAR’: No such file or directory
rm: cannot remove ‘PROCAR’: No such file or directory
rm: cannot remove ‘DOSCAR’: No such file or directory
rm: cannot remove ‘OSZICAR’: No such file or directory
rm: cannot remove ‘PCDAT’: No such file or directory
rm: cannot remove ‘REPORT’: No such file or directory
rm: cannot remove ‘XDATCAR’: No such file or directory
rm: cannot remove ‘vasprun.xml’: No such file or directory
rm: cannot remove ‘RUNNING’: No such file or directory 

-- To read results use  res_loop('Li', ['static'], [1], show = 'fo'  )     # , on 2019-06-27   ; possible options for show: fit, fo, fop, en, mag, magp, smag, maga, occ, occ1, mep, mepp 

-- Opening  only_calc.gdbm3 for writing 

-- saving key: ('Li', 'static', 1) 


End of work at 2019-06-27 18:46:13.241557
 


Launch at 2019-06-27 18:48:39.455381
 

-- You provided the following geo file explicitly  Li.POSCAR ; Version of file does not matter, I use *curver*= 1 as a new version 

-- vasp  format is detected 

-- Vasp4 detected 

I take elements from the first line, The line is ['i2a=[Li] ; Li2.static.1'] you could use ! to add comment after name+
 

-- i2a list detected 

The following Z were read = [3]
 

VASP POSCAR format Li.POSCAR  was read
 

-- We use sd cluster 

-- Running pwd on server ... 

-- /home/aksenov 

-- The home folder on cluster is  /home/aksenov 

-- add_loop: starting add_loop_inherit ... 

-- add_calculation(): Li.static.1  has been already created and has state:  2. Ready for start 

-- check_kpoints(): k-points will be used from *ngkpt_dict* of Li [9, 9, 9] 

-- check_kpoints(): Kpoint   mesh is:  [9, 9, 9] 

-- check_kpoints(): The actual k-spacings are  [ 0.23  0.23  0.23] 

-- remove_atoms(): Atoms ['void'] were removed 

-- Starting writing POSCAR Li//Li.static/1.POSCAR Vasp5: True 

-- POSCAR was written to /hdd/home/aksenov/Simulation_wrapper/siman/tutorials/test/Li//Li.static/1.POSCAR 

-- The value of savefile is oc 

-- Potentials from  /hdd/home/aksenov/scientific_projects/PAW_PBE_VASP are taken 

-- POTCAR files: ['/hdd/home/aksenov/scientific_projects/PAW_PBE_VASP/Li/POTCAR'] 

-- remove_atoms(): Atoms ['void'] were removed 

-- I found that at least 1  bands are required. I will use 1 bands; add_nbands =  1.25 

Li//Li.static/INCAR was generated
 

You said to generate KPOINTS file.
 

-- Attention! ngkpt =  [9, 9, 9]  is adopted from struct_des which you provided for it  Li  and kspacing =  0.235 

KPOINTS was generated
 

-- Files to copy: ['Li//Li.static/INCAR', 'Li//Li.static/KPOINTS', 'Li//Li.static/Li.static.run', 'Li//Li.static/POTCAR', 'Li//Li.static/1.POSCAR'] 

-- Running  mkdir -p /home/aksenov//Li//Li.static/ on server ... 

--  

-- push_to_server():  mkdir -p /home/aksenov//Li//Li.static/  

-- push_to_server(): uploading files  ['Li//Li.static/INCAR', 'Li//Li.static/KPOINTS', 'Li//Li.static/Li.static.run', 'Li//Li.static/POTCAR', 'Li//Li.static/1.POSCAR'] to sd /home/aksenov//Li//Li.static/ 

--  

-- Setting executable rights for batch script on server /home/aksenov//Li//Li.static/Li.static.run 

-- Running chmod +x /home/aksenov//Li//Li.static/Li.static.run on server ... 

--  


Run file created
 


Calculation ('Li', 'static', 1) successfully created

 

-- Running  mkdir -p /home/aksenov on server ... 

--  

-- push_to_server():  mkdir -p /home/aksenov  

-- push_to_server(): uploading files  ['run'] to sd /home/aksenov 

--  

-- Running chmod +x run on server ... 

--  

-- run sent 

-- Running ./run on server ... 

/home/AMG/vasp/vasp: error while loading shared libraries: libmkl_intel_lp64.so: cannot open shared object file: No such file or directory
/home/AMG/vasp/vasp: error while loading shared libraries: libmkl_intel_lp64.so: cannot open shared object file: No such file or directory
--------------------------------------------------------------------------
mpirun noticed that the job aborted, but has no info as to the process
that caused that situation.
--------------------------------------------------------------------------
rm: cannot remove ‘PROCAR’: No such file or directory
rm: cannot remove ‘RUNNING’: No such file or directory 

/home/AMG/vasp/vasp: error while loading shared libraries: libmkl_intel_lp64.so: cannot open shared object file: No such file or directory
/home/AMG/vasp/vasp: error while loading shared libraries: libmkl_intel_lp64.so: cannot open shared object file: No such file or directory
--------------------------------------------------------------------------
mpirun noticed that the job aborted, but has no info as to the process
that caused that situation.
--------------------------------------------------------------------------
rm: cannot remove ‘PROCAR’: No such file or directory
rm: cannot remove ‘RUNNING’: No such file or directory 

-- To read results use  res_loop('Li', ['static'], [1], show = 'fo'  )     # , on 2019-06-27   ; possible options for show: fit, fo, fop, en, mag, magp, smag, maga, occ, occ1, mep, mepp 


Launch at 2019-06-27 18:50:18.404024
 

-- You provided the following geo file explicitly  Li.POSCAR ; Version of file does not matter, I use *curver*= 1 as a new version 

-- vasp  format is detected 

-- Vasp4 detected 

I take elements from the first line, The line is ['i2a=[Li] ; Li2.static.1'] you could use ! to add comment after name+
 

-- i2a list detected 

The following Z were read = [3]
 

VASP POSCAR format Li.POSCAR  was read
 

-- We use sd cluster 

-- Running pwd on server ... 

-- /home/aksenov 

-- The home folder on cluster is  /home/aksenov 

-- add_loop: starting add_loop_inherit ... 

-- add_calculation(): Li.static.1  has been already created and has state:  2. Ready for start 

-- check_kpoints(): k-points will be used from *ngkpt_dict* of Li [9, 9, 9] 

-- check_kpoints(): Kpoint   mesh is:  [9, 9, 9] 

-- check_kpoints(): The actual k-spacings are  [ 0.23  0.23  0.23] 

-- remove_atoms(): Atoms ['void'] were removed 

-- Starting writing POSCAR Li//Li.static/1.POSCAR Vasp5: True 

-- POSCAR was written to /hdd/home/aksenov/Simulation_wrapper/siman/tutorials/test/Li//Li.static/1.POSCAR 

-- The value of savefile is oc 

-- Potentials from  /hdd/home/aksenov/scientific_projects/PAW_PBE_VASP are taken 

-- POTCAR files: ['/hdd/home/aksenov/scientific_projects/PAW_PBE_VASP/Li/POTCAR'] 

-- remove_atoms(): Atoms ['void'] were removed 

-- I found that at least 1  bands are required. I will use 1 bands; add_nbands =  1.25 

Li//Li.static/INCAR was generated
 

You said to generate KPOINTS file.
 

-- Attention! ngkpt =  [9, 9, 9]  is adopted from struct_des which you provided for it  Li  and kspacing =  0.235 

KPOINTS was generated
 

-- Files to copy: ['Li//Li.static/INCAR', 'Li//Li.static/KPOINTS', 'Li//Li.static/Li.static.run', 'Li//Li.static/POTCAR', 'Li//Li.static/1.POSCAR'] 

-- Running  mkdir -p /home/aksenov//Li//Li.static/ on server ... 

--  

-- push_to_server():  mkdir -p /home/aksenov//Li//Li.static/  

-- push_to_server(): uploading files  ['Li//Li.static/INCAR', 'Li//Li.static/KPOINTS', 'Li//Li.static/Li.static.run', 'Li//Li.static/POTCAR', 'Li//Li.static/1.POSCAR'] to sd /home/aksenov//Li//Li.static/ 

--  

-- Setting executable rights for batch script on server /home/aksenov//Li//Li.static/Li.static.run 

-- Running chmod +x /home/aksenov//Li//Li.static/Li.static.run on server ... 

--  


Run file created
 


Calculation ('Li', 'static', 1) successfully created

 

-- Running  mkdir -p /home/aksenov on server ... 

--  

-- push_to_server():  mkdir -p /home/aksenov  

-- push_to_server(): uploading files  ['run'] to sd /home/aksenov 

--  

-- Running chmod +x run on server ... 

--  

-- run sent 

-- Running ./run on server ... 

rm: cannot remove ‘PROCAR’: No such file or directory
rm: cannot remove ‘RUNNING’: No such file or directory 

rm: cannot remove ‘PROCAR’: No such file or directory
rm: cannot remove ‘RUNNING’: No such file or directory 

-- To read results use  res_loop('Li', ['static'], [1], show = 'fo'  )     # , on 2019-06-27   ; possible options for show: fit, fo, fop, en, mag, magp, smag, maga, occ, occ1, mep, mepp 

-- Attention! unknown SCHEDULE_SYSTEM=none; Please teach me here!  

-- Checking existence of file Li//Li.static/RUNNING on server sd 

-- Running  ls Li//Li.static/RUNNING on server ... 

-- ls: cannot access Li//Li.static/RUNNING: No such file or directory 

-- File exist?  False 

-- Starting self.read_results() ... 

-- read_results() path to outcar Li//Li.static/1.OUTCAR 

-- The load flag is  o 

-- Trying to download /home/aksenov//Li//Li.static/1.OUTCAR from server 

-- Checking existence of file /home/aksenov//Li//Li.static/1.OUTCAR on server sd 

-- Running  ls /home/aksenov//Li//Li.static/1.OUTCAR on server ... 

-- /home/aksenov//Li//Li.static/1.OUTCAR 

-- File exist?  True 

-- Using paramiko: ssh_object.get(): from  to  /home/aksenov//Li//Li.static/1.OUTCAR Li//Li.static/1.OUTCAR 

-- Download result is  OK 

-- File Li//Li.static/1.OUTCAR  was download 

-- Trying to download /home/aksenov//Li//Li.static/1.CONTCAR from server 

-- Checking existence of file /home/aksenov//Li//Li.static/1.CONTCAR on server sd 

-- Running  ls /home/aksenov//Li//Li.static/1.CONTCAR on server ... 

-- /home/aksenov//Li//Li.static/1.CONTCAR 

-- File exist?  True 

-- Using paramiko: ssh_object.get(): from  to  /home/aksenov//Li//Li.static/1.CONTCAR Li//Li.static/1.CONTCAR 

-- Download result is  OK 

-- File Li//Li.static/1.CONTCAR  was download 

-- The grep result of Li//Li.static/1.OUTCAR is: General timing and accounting informations for this job: 

-- Path to CONTCAR Li//Li.static/1.CONTCAR 

-- The status of CONTCAR file is True 

-- Vasp5 detected 

-- elements_list: ['Li'] 

Elements names have been taken from the end of coordinates, pymatgen file?
 

The following Z were read = [3]
 

VASP POSCAR format Li//Li.static/1.CONTCAR  was read
 

-- Start reading from Li//Li.static/1.OUTCAR 

-- You provided the following geo file explicitly  Li.POSCAR ; Version of file does not matter, I use *curver*= 1 as a new version 

-- vasp  format is detected 

-- Vasp4 detected 

I take elements from the first line, The line is ['i2a=[Li] ; Li2.static.1'] you could use ! to add comment after name+
 

-- i2a list detected 

The following Z were read = [3]
 

VASP POSCAR format Li.POSCAR  was read
 

-- We use sd cluster 

-- Running pwd on server ... 

-- /home/aksenov 

-- The home folder on cluster is  /home/aksenov 

-- add_loop: starting add_loop_inherit ... 

-- add_calculation(): Li.static.1  has been already created and has state:  4. Finished 

-- Attention! unknown SCHEDULE_SYSTEM=none; Please teach me here!  

-- Checking existence of file Li//Li.static/RUNNING on server sd 

-- Running  ls Li//Li.static/RUNNING on server ... 

-- ls: cannot access Li//Li.static/RUNNING: No such file or directory 

-- File exist?  False 

-- Starting self.read_results() ... 

-- read_results() path to outcar Li//Li.static/1.OUTCAR 

-- The load flag is   

-- The grep result of Li//Li.static/1.OUTCAR is: General timing and accounting informations for this job: 

-- Path to CONTCAR Li//Li.static/1.CONTCAR 

-- The status of CONTCAR file is True 

-- Vasp5 detected 

-- elements_list: ['Li'] 

Elements names have been taken from the end of coordinates, pymatgen file?
 

The following Z were read = [3]
 

VASP POSCAR format Li//Li.static/1.CONTCAR  was read
 

-- Start reading from Li//Li.static/1.OUTCAR 


Launch at 2019-06-27 18:53:46.299097
 

-- You provided the following geo file explicitly  Li.POSCAR ; Version of file does not matter, I use *curver*= 1 as a new version 

-- vasp  format is detected 

-- Vasp4 detected 

I take elements from the first line, The line is ['i2a=[Li] ; Li2.static.1'] you could use ! to add comment after name+
 

-- i2a list detected 

The following Z were read = [3]
 

VASP POSCAR format Li.POSCAR  was read
 

-- We use sd cluster 

-- Running pwd on server ... 

-- /home/aksenov 

-- The home folder on cluster is  /home/aksenov 

-- add_loop: starting add_loop_inherit ... 

-- add_calculation(): Li.static.1  has been already created and has state:  2. Ready for start 

-- check_kpoints(): k-points will be used from *ngkpt_dict* of Li [9, 9, 9] 

-- check_kpoints(): Kpoint   mesh is:  [9, 9, 9] 

-- check_kpoints(): The actual k-spacings are  [ 0.23  0.23  0.23] 

-- remove_atoms(): Atoms ['void'] were removed 

-- Starting writing POSCAR Li//Li.static/1.POSCAR Vasp5: True 

-- POSCAR was written to /hdd/home/aksenov/Simulation_wrapper/siman/tutorials/test/Li//Li.static/1.POSCAR 

-- The value of savefile is oc 

-- Potentials from  /hdd/home/aksenov/scientific_projects/PAW_PBE_VASP are taken 

-- POTCAR files: ['/hdd/home/aksenov/scientific_projects/PAW_PBE_VASP/Li/POTCAR'] 

-- remove_atoms(): Atoms ['void'] were removed 

-- I found that at least 1  bands are required. I will use 1 bands; add_nbands =  1.25 

Li//Li.static/INCAR was generated
 

You said to generate KPOINTS file.
 

-- Attention! ngkpt =  [9, 9, 9]  is adopted from struct_des which you provided for it  Li  and kspacing =  0.235 

KPOINTS was generated
 

-- Files to copy: ['Li//Li.static/INCAR', 'Li//Li.static/KPOINTS', 'Li//Li.static/Li.static.run', 'Li//Li.static/POTCAR', 'Li//Li.static/1.POSCAR'] 

-- Running  mkdir -p /home/aksenov//Li//Li.static/ on server ... 

--  

-- push_to_server():  mkdir -p /home/aksenov//Li//Li.static/  

-- push_to_server(): uploading files  ['Li//Li.static/INCAR', 'Li//Li.static/KPOINTS', 'Li//Li.static/Li.static.run', 'Li//Li.static/POTCAR', 'Li//Li.static/1.POSCAR'] to sd /home/aksenov//Li//Li.static/ 

--  

-- Setting executable rights for batch script on server /home/aksenov//Li//Li.static/Li.static.run 

-- Running chmod +x /home/aksenov//Li//Li.static/Li.static.run on server ... 

--  


Run file created
 


Calculation ('Li', 'static', 1) successfully created

 

-- Running  mkdir -p /home/aksenov on server ... 

--  

-- push_to_server():  mkdir -p /home/aksenov  

-- push_to_server(): uploading files  ['run'] to sd /home/aksenov 

--  

-- Running chmod +x run on server ... 

--  

-- run sent 

-- Running ./run on server ... 

rm: cannot remove ‘PROCAR’: No such file or directory
rm: cannot remove ‘RUNNING’: No such file or directory 

rm: cannot remove ‘PROCAR’: No such file or directory
rm: cannot remove ‘RUNNING’: No such file or directory 

-- To read results use  res_loop('Li', ['static'], [1], show = 'fo'  )     # , on 2019-06-27   ; possible options for show: fit, fo, fop, en, mag, magp, smag, maga, occ, occ1, mep, mepp 

-- Checking existence of file Li//Li.static/RUNNING on server sd 

-- Running  ls Li//Li.static/RUNNING on server ... 

-- ls: cannot access Li//Li.static/RUNNING: No such file or directory 

-- File exist?  False 

-- Starting self.read_results() ... 

-- read_results() path to outcar Li//Li.static/1.OUTCAR 

-- The load flag is   

-- The grep result of Li//Li.static/1.OUTCAR is: General timing and accounting informations for this job: 

-- Path to CONTCAR Li//Li.static/1.CONTCAR 

-- The status of CONTCAR file is True 

-- Vasp5 detected 

-- elements_list: ['Li'] 

Elements names have been taken from the end of coordinates, pymatgen file?
 

The following Z were read = [3]
 

VASP POSCAR format Li//Li.static/1.CONTCAR  was read
 

-- Start reading from Li//Li.static/1.OUTCAR 


Launch at 2019-06-27 18:55:25.444901
 

-- You provided the following geo file explicitly  Li.POSCAR ; Version of file does not matter, I use *curver*= 1 as a new version 

-- vasp  format is detected 

-- Vasp4 detected 

I take elements from the first line, The line is ['i2a=[Li] ; Li2.static.1'] you could use ! to add comment after name+
 

-- i2a list detected 

The following Z were read = [3]
 

VASP POSCAR format Li.POSCAR  was read
 

-- We use sd cluster 

-- Running pwd on server ... 

-- /home/aksenov 

-- The home folder on cluster is  /home/aksenov 

-- add_loop: starting add_loop_inherit ... 

-- add_calculation(): Li.static.1  has been already created and has state:  2. Ready for start 

-- check_kpoints(): k-points will be used from *ngkpt_dict* of Li [9, 9, 9] 

-- check_kpoints(): Kpoint   mesh is:  [9, 9, 9] 

-- check_kpoints(): The actual k-spacings are  [ 0.23  0.23  0.23] 

-- remove_atoms(): Atoms ['void'] were removed 

-- Starting writing POSCAR Li//Li.static/1.POSCAR Vasp5: True 

-- POSCAR was written to /hdd/home/aksenov/Simulation_wrapper/siman/tutorials/test/Li//Li.static/1.POSCAR 

-- The value of savefile is oc 

-- Potentials from  /hdd/home/aksenov/scientific_projects/PAW_PBE_VASP are taken 

-- POTCAR files: ['/hdd/home/aksenov/scientific_projects/PAW_PBE_VASP/Li/POTCAR'] 

-- remove_atoms(): Atoms ['void'] were removed 

-- I found that at least 1  bands are required. I will use 1 bands; add_nbands =  1.25 

Li//Li.static/INCAR was generated
 

You said to generate KPOINTS file.
 

-- Attention! ngkpt =  [9, 9, 9]  is adopted from struct_des which you provided for it  Li  and kspacing =  0.235 

KPOINTS was generated
 

-- Files to copy: ['Li//Li.static/INCAR', 'Li//Li.static/KPOINTS', 'Li//Li.static/Li.static.run', 'Li//Li.static/POTCAR', 'Li//Li.static/1.POSCAR'] 

-- Running  mkdir -p /home/aksenov//Li//Li.static/ on server ... 

--  

-- push_to_server():  mkdir -p /home/aksenov//Li//Li.static/  

-- push_to_server(): uploading files  ['Li//Li.static/INCAR', 'Li//Li.static/KPOINTS', 'Li//Li.static/Li.static.run', 'Li//Li.static/POTCAR', 'Li//Li.static/1.POSCAR'] to sd /home/aksenov//Li//Li.static/ 

--  

-- Setting executable rights for batch script on server /home/aksenov//Li//Li.static/Li.static.run 

-- Running chmod +x /home/aksenov//Li//Li.static/Li.static.run on server ... 

--  


Run file created
 


Calculation ('Li', 'static', 1) successfully created

 

-- Running  mkdir -p /home/aksenov on server ... 

--  

-- push_to_server():  mkdir -p /home/aksenov  

-- push_to_server(): uploading files  ['run'] to sd /home/aksenov 

--  

-- Running chmod +x run on server ... 

--  

-- run sent 

-- Running ./run on server ... 

rm: cannot remove ‘PROCAR’: No such file or directory
rm: cannot remove ‘RUNNING’: No such file or directory 

rm: cannot remove ‘PROCAR’: No such file or directory
rm: cannot remove ‘RUNNING’: No such file or directory 

-- To read results use  res_loop('Li', ['static'], [1], show = 'fo'  )     # , on 2019-06-27   ; possible options for show: fit, fo, fop, en, mag, magp, smag, maga, occ, occ1, mep, mepp 

-- Checking existence of file Li//Li.static/RUNNING on server sd 

-- Running  ls Li//Li.static/RUNNING on server ... 

-- ls: cannot access Li//Li.static/RUNNING: No such file or directory 

-- File exist?  False 

-- Starting self.read_results() ... 

-- read_results() path to outcar Li//Li.static/1.OUTCAR 

-- The load flag is   

-- The grep result of Li//Li.static/1.OUTCAR is: General timing and accounting informations for this job: 

-- Path to CONTCAR Li//Li.static/1.CONTCAR 

-- The status of CONTCAR file is True 

-- Vasp5 detected 

-- elements_list: ['Li'] 

Elements names have been taken from the end of coordinates, pymatgen file?
 

The following Z were read = [3]
 

VASP POSCAR format Li//Li.static/1.CONTCAR  was read
 

-- Start reading from Li//Li.static/1.OUTCAR 

-- Checking existence of file Li//Li.static/RUNNING on server sd 

-- Running  ls Li//Li.static/RUNNING on server ... 

-- ls: cannot access Li//Li.static/RUNNING: No such file or directory 

-- File exist?  False 

-- Starting self.read_results() ... 

-- read_results() path to outcar Li//Li.static/1.OUTCAR 

-- The load flag is  up2o 

-- Trying to download /home/aksenov//Li//Li.static/1.OUTCAR from server 

-- Checking existence of file /home/aksenov//Li//Li.static/1.OUTCAR on server sd 

-- Running  ls /home/aksenov//Li//Li.static/1.OUTCAR on server ... 

-- /home/aksenov//Li//Li.static/1.OUTCAR 

-- File exist?  True 

-- Using paramiko: ssh_object.get(): from  to  /home/aksenov//Li//Li.static/1.OUTCAR Li//Li.static/1.OUTCAR 

-- Download result is  OK 

-- File Li//Li.static/1.OUTCAR  was download 

-- Trying to download /home/aksenov//Li//Li.static/1.CONTCAR from server 

-- Checking existence of file /home/aksenov//Li//Li.static/1.CONTCAR on server sd 

-- Running  ls /home/aksenov//Li//Li.static/1.CONTCAR on server ... 

-- /home/aksenov//Li//Li.static/1.CONTCAR 

-- File exist?  True 

-- Using paramiko: ssh_object.get(): from  to  /home/aksenov//Li//Li.static/1.CONTCAR Li//Li.static/1.CONTCAR 

-- Download result is  OK 

-- File Li//Li.static/1.CONTCAR  was download 

-- The grep result of Li//Li.static/1.OUTCAR is: General timing and accounting informations for this job: 

-- Path to CONTCAR Li//Li.static/1.CONTCAR 

-- The status of CONTCAR file is True 

-- Vasp5 detected 

-- elements_list: ['Li'] 

Elements names have been taken from the end of coordinates, pymatgen file?
 

The following Z were read = [3]
 

VASP POSCAR format Li//Li.static/1.CONTCAR  was read
 

-- Start reading from Li//Li.static/1.OUTCAR 

Warning! TOO FEW BANDS!!!


Warning! TOO FEW BANDS!!!
 



Max. F. tot  (meV/A) = 
[0]; 

Reading of results completed

 

-- Output type: outst_cathode 

-- read_results() output  Im-3m |  -3.1414   |  -1.5707   |3.00;3.00;3.00|  27.0  |  35 | 11854,11854,11854  | 2  | 0.000  |   1,10, 10   |  4  | 48| 0.0 |  -0| -3.1  

-- db['Li.static.1']             | Im-3m |  -3.1414   |  -1.5707   |3.00;3.00;3.00|  27.0  |  35 | 11854,11854,11854  | 2  | 0.000  |   1,10, 10   |  4  | 48| 0.0 |  -0| -3.1  
-- Opening  only_calc.gdbm3 for writing 

-- saving key: ('Li', 'static', 1) 


End of work at 2019-06-27 18:56:58.692211