[SIESTA-L] band structure and PDOS of the central molecule of device

[ANKITA JOSHI]

Dear SIESTA users,

I want to determine band structure and PDOS of only central molecule in a
device. Does anyone know how to make the input files? Please give any
suggestions.

Thanks
Ankita

[SIESTA-L] Band structure calculations

[ANKITA JOSHI]

Dear SIESTA users,

I am bit confused regarding the band structure calculations. The procedure
followed to calculate band structure is:

1. First I did full relaxation of the system electrode-molecule-electrode.
2. Then, using the optimized coordinates of the system
electrode-molecule-molecule, I have done the band structure calculations.

Is this the correct approach? Also, how to do the band structure
calculation only for the scattering region?

Thanks
Ankita

[SIESTA-L] error in eigenvalue obtained from MPSH calculation

[Ankita Joshi]

Dear SIESTA users,
I have done MPSH calculation for my system and the attached (scat.EIGVAL)) file 
is generated. I want to find HOMO and LUMO from this file which should be the 
lowest negative and positive eigenvalue, respectively. However, all the 
eigenvalues obtained is found to be negative. Can anyone please go through the 
file and give any suggestion?


Thanks 
Ankita
# Device region = [73,168], units in eV
0 -670.46638770
1 -670.24427890
2 -668.85350103
3 -668.14667508
4 -667.14619719
5 -666.20889306
6 -665.14805883
7 -663.89063625
8 -662.92642335
9 -661.83775317
10 -660.77476955
11 -659.43371325
12 -658.31085781
13 -657.14521199
14 -655.97029466
15 -654.80318410
16 -653.75251238
17 -652.64227181
18 -652.00756568
19 -651.64368995
20 -651.11590034
21 -650.31272256
22 -650.16715353
23 -649.73980055
24 -649.62298396
25 -648.83209710
26 -648.46321231
27 -648.28523545
28 -647.84672237
29 -647.20176149
30 -647.04405699
31 -646.86400289
32 -646.50589402
33 -645.99292347
34 -645.77754161
35 -645.47900525
36 -644.13219737
37 -643.17037086
38 -640.35378466
39 -640.13932835
40 -639.81874177
41 -639.72085597
42 -639.04139671
43 -638.08054156
44 -637.61358337
45 -637.21998481
46 -636.75901479
47 -635.45512548
48 -635.10230609
49 -634.75455513
50 -634.68283773
51 -634.26213615
52 -634.04476614
53 -633.89631857
54 -633.70522065
55 -633.68500012
56 -633.39091438
57 -633.20598002
58 -632.70616951
59 -632.41634761
60 -632.33609986
61 -631.92880976
62 -631.77319602
63 -631.63412611
64 -631.53916111
65 -631.20750561
66 -630.05877360
67 -629.91108054
68 -629.68839383
69 -629.53542000
70 -629.03861514
71 -628.81110963
72 -628.23851100
73 -627.40963870
74 -626.59542730
75 -626.12048758
76 -625.77334543
77 -625.44419066
78 -625.25752132
79 -625.03958094
80 -624.44787587
81 -624.37446547
82 -623.90538188
83 -623.54550041
84 -623.29825719
85 -622.65250769
86 -622.53348123
87 -622.13820288
88 -621.12427239
89 -620.82529654
90 -620.41319892
91 -620.14669805
92 -619.13952289
93 -618.67643906
94 -618.42739529
95 -618.15476460
96 -617.67515454
97 -617.46006592
98 -617.36550915
99 -617.18916710
100 -616.67594741
101 -616.39578283
102 -616.15085268
103 -615.66435133
104 -615.16193917
105 -615.11008274
106 -614.93458045
107 -614.81246167
108 -614.61975332
109 -614.02139827
110 -613.85716625
111 -613.69743310
112 -613.02318367
113 -612.83688704
114 -612.67918899
115 -612.50480397
116 -612.46112223
117 -612.11213775
118 -612.05436098
119 -611.96335322
120 -611.48243186
121 -611.11146234
122 -611.07931417
123 -610.68893923
124 -609.46497963
125 -609.29940669
126 -608.80358597
127 -608.66998094
128 -608.57735547
129 -608.31438087
130 -608.03766639
131 -607.87136202
132 -607.79014309
133 -607.63083600
134 -607.51650700
135 -607.16090469
136 -606.93599300
137 -606.53441082
138 -606.27037944
139 -605.98230461
140 -605.94413965
141 -605.66386499
142 -605.26175007
143 -604.97044325
144 -604.77716537
145 -604.65000494
146 -604.21000432
147 -603.74008102
148 -603.23854487
149 -602.86520734
150 -602.43823316
151 -602.41468374
152 -601.80966881
153 -601.59418127
154 -601.38716324
155 -601.29433379
156 -601.04561852
157 -600.81803117
158 -600.61978305
159 -600.50638632
160 -600.40615388
161 -600.09623569
162 -599.97407428
163 -599.89912596
164 -599.57122533
165 -599.46964803
166 -599.41324641
167 -599.15394837
168 -599.00290083
169 -598.85881462
170 -598.60077695
171 -598.43533677
172 -598.36174717
173 -597.69778922
174 -597.08491583
175 -596.86572942
176 -596.47348439
177 -595.89108870
178 -595.57860198
179 -594.95728622
180 -594.84947117
181 -594.73727691
182 -594.29018301
183 -593.88902524
184 -593.64938061
185 -593.35459664
186 -592.86385989
187 -592.20533181
188 -591.87129913
189 -591.34037876
190 -591.05577590
191 -590.92150317
192 -590.56333551
193 -590.40762790
194 -590.06243164
195 -589.94353620
196 -589.77731265
197 -589.72197503
198 -589.58643749
199 -589.55148193
200 -589.45330491
201 -589.14243590
202 -588.90205992
203 -588.30860415
204 -587.76808922
205 -587.60347708
206 -587.08712660
207 -586.99097234
208 -586.79473710
209 -586.63756153
210 -586.36630393
211 -586.07394108
212 -585.76571447
213 -585.51630791
214 -585.46803084
215 -585.38820880
216 -585.22294453
217 -584.98850882
218 -584.77910666
219 -584.56637138
220 -584.40656733
221 -584.27298817
222 -584.26606183
223 -583.90522872
224 -583.82633175
225 -583.50397829
226 -583.43495803
227 -583.06796999
228 -582.66103626
229 -582.55824841
230 -581.8436
231 -581.37891005
232 -581.19828198
233 -580.93710572
234 -580.72799372
235 -580.57739089
236 -579.97917039
237 -579.88513783
238 -579.78013946
239 -579.56672718
240 -579.40852638
241 -579.13175120
242 -578.87032937
243 -578.51842989
244 -578.39230840
245 -577.93593028
246 -577.79791441
247 -577.56952966
248 -577.43207834
249 -577.08894015
250 -576.66072787
251 -576.35163104
252 -575.81729068
253 -574.68153326
254 -574.09321613
255 -573.66041629
256 -573.63208582
257 -573.43090941
258 -573.19527885
259 -572.63483881
260 

[SIESTA-L] MPSH state of HOMO and LUMO in the scatttering region

[Ankita Joshi]

Dear SIESTA users,


I am using INELASTICA software to determine MPSH state of HOMO and LUMO in the 
scattering region. I tried few commands like:


EigenChannels -n 0 -f ./*fdf -M 3.0 EIG 


By using this command, files like scat.S*.E0.*.XSF, scat.S*.E1.*.XSF and 
scat.S*.E2.*XSF where * corresponds to different values, were generated. 


EIGEigenChannels -f ./*fdf EIG


By using this command, files like scat.EC.1L.XSF, scat.EC.2L.XSF, 
scat.EC.3L.XSF and scat.EC.4L.XSF, were generated.



Since I am new to this software, I don't know what does this mean. Can anybody 
please explain this to me?


Thanks
Ankita

Re: [SIESTA-L] Error in running grid2cube

[Ankita Joshi]

Thanks everyone. As per the suggestions, the problem is solved now by 
increasing the parameter maxp.

On 07/08/18, Nick Papior   wrote:
> There is a constant "maxp" in the grid2cube.f utility file. Simply increase 
> the number to something bigger than your used grid size, recompile the 
> utility and redo the grid2cube command.
> 
> Den søn. 5. aug. 2018 kl. 22.01 skrev Ankita Joshi :
> 
> 
> > Dear Siesta Users,
> > 
> > 
> > While plotting LDOS for my system using a post-processing tool grid2cube, I 
> > encountered following error:
> > STOP grid2d: Parameter MAXP too small
> > 
> > 
> > Does anyone knows how to solve this problem? Please give your suggestions. 
> > 
> > 
> > Thanks
> > Ankita
> >  
> 
> 
> 
> 
> -- 
> Kind regards Nick
> 
> 
>  
>

[SIESTA-L] Error in running grid2cube

[Ankita Joshi]

Dear Siesta Users,


While plotting LDOS for my system using a post-processing tool grid2cube, I 
encountered following error:
STOP grid2d: Parameter MAXP too small


Does anyone knows how to solve this problem? Please give your suggestions. 


Thanks
Ankita

Re: [SIESTA-L] Error in installing tbtrans with netcdf4 support in cluster using intel compiler

[Ankita Joshi]

Dear Nick,

Now it's working. 

Thanks
Ankita





On 23/01/18, Nick Papior  <nickpap...@gmail.com> wrote:




> You haven't added the netcdf libraries to the linker lines...
> 
> 
> Please check your arch.make file.
> 
> 
> 2018-01-21 7:59 GMT+01:00 Ankita Joshi <joshi.dcy2...@iitr.ac.in>:
> 
> > Dear Nick,
> > 
> > 
> > Thanks for your response. As per the suggestion, I have installed NetCDF4 
> > with intel compiler but still getting another error as enclosed in a file 
> > named "error.log". Please suggest something. Looking forward for your 
> > response.
> > 
> > 
> > Thanks
> > Ankita
> > 
> > On 19/01/18, Ankita Joshi  <joshi.dcy2...@iitr.ac.in> wrote:
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > > Dear Nick,
> > > 
> > > 
> > > I am facing difficulty in installing tbtrans with netcdf4 support in 
> > > cluster using intel compilers. On using COMP_LIBS += libncdf.a and 
> > > FPPFLAGS += -DCDF -DNCDF -DNCDF_4 in arch.make file, the following errors 
> > > were found:
> > > 
> > > 
> > > netcdf_ncdf.f90(59): error #7013: This module file was not generated by 
> > > any release of this compiler. [NETCDF]
> > >  use netcdf
> > > 
> > > 
> > > ...
> > > 
> > > netcdf_ncdf.f90(2995): catastrophic error: Too many errors, exiting
> > > compilation aborted for netcdf_ncdf.f90 (code 1)
> > > make[1]: *** [netcdf_ncdf.o] Error 1
> > > make[1]: Leaving directory 
> > > `/UHOME/joshi.dcy2014/SOFTWARE/SIESTA/INTEL/Parrallel/TBTRANS/tbtrans_18-01-2018/Obj/ncdf/obj'
> > > make: *** [libncdf.a] Error 2
> > > 
> > > 
> > > 
> > > 
> > > I have attached my arch.make file.
> > > Could you please suggest me something? Any help would be greatly 
> > > appreciated.
> > > 
> > > 
> > > 
> > > Thanks
> > > Ankita
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > >  
> > > 
> >  
> > 
> > 
> 
> 
> 
> 
> 
> -- 
> Kind regards Nick
> 
> 
>  
> 
>  
> 

[SIESTA-L] Error in installing tbtrans with netcdf4 support in cluster using intel compiler

[Ankita Joshi]

Dear Nick,

I am facing difficulty in installing tbtrans with netcdf4 support in cluster 
using intel compilers. On using COMP_LIBS += libncdf.a and FPPFLAGS += -DCDF 
-DNCDF -DNCDF_4 in arch.make file, the following errors were found:

netcdf_ncdf.f90(59): error #7013: This module file was not generated by any 
release of this compiler. [NETCDF]
 use netcdf

...

netcdf_ncdf.f90(2995): catastrophic error: Too many errors, exiting
compilation aborted for netcdf_ncdf.f90 (code 1)
make[1]: *** [netcdf_ncdf.o] Error 1
make[1]: Leaving directory 
`/UHOME/joshi.dcy2014/SOFTWARE/SIESTA/INTEL/Parrallel/TBTRANS/tbtrans_18-01-2018/Obj/ncdf/obj'
make: *** [libncdf.a] Error 2


I have attached my arch.make file.
Could you please suggest me something? Any help would be greatly appreciated.


Thanks
Ankita
#
# This file is part of the SIESTA package.
#
# Copyright (c) Fundacion General Universidad Autonoma de Madrid:
# E.Artacho, J.Gale, A.Garcia, J.Junquera, P.Ordejon, D.Sanchez-Portal
# and J.M.Soler, 1996- .
#
# Use of this software constitutes agreement with the full conditions
# given in the SIESTA license, as signed by all legitimate users.
#
.SUFFIXES:
.SUFFIXES: .f .F .o .a .f90 .F90

SIESTA_ARCH=x86_64-unknown-linux-gnu--unknown

FPP = 
FPP_OUTPUT=
FC=mpiifort
F90=mpiifort
FC_SERIAL = ifort
RANLIB=ranlib


SYS=nag

SP_KIND=4
DP_KIND=8
KINDS=$(SP_KIND) $(DP_KIND)

FFLAGS=-g
FPPFLAGS= -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT
LDFLAGS=

ARFLAGS_EXTRA=

#FCFLAGS_fixed_f=
#FCFLAGS_free_f90=
#FPPFLAGS_fixed_F=
#FPPFLAGS_free_F90=

BLAS_LIBS=-Wl,--start-group 
/SOFT/ics_2013.1.046/composer_xe_2013_sp1.2.144/mkl/lib/intel64/libmkl_intel_lp64.a
 
/SOFT/ics_2013.1.046/composer_xe_2013_sp1.2.144/mkl/lib/intel64/libmkl_sequential.a
 /SOFT/ics_2013.1.046/composer_xe_2013_sp1.2.144/mkl/lib/intel64/libmkl_core.a  
 -Wl,--end-group

LAPACK_LIBS=-Wl,--start-group 
/SOFT/ics_2013.1.046/composer_xe_2013_sp1.2.144/mkl/lib/intel64/libmkl_intel_lp64.a
 
/SOFT/ics_2013.1.046/composer_xe_2013_sp1.2.144/mkl/lib/intel64/libmkl_sequential.a
 /SOFT/ics_2013.1.046/composer_xe_2013_sp1.2.144/mkl/lib/intel64/libmkl_core.a  
-Wl,--end-group

BLACS_LIBS=-Wl,--start-group 
/SOFT/ics_2013.1.046/composer_xe_2013_sp1.2.144/mkl/lib/intel64/libmkl_intel_lp64.a
 
/SOFT/ics_2013.1.046/composer_xe_2013_sp1.2.144/mkl/lib/intel64/libmkl_sequential.a
 /SOFT/ics_2013.1.046/composer_xe_2013_sp1.2.144/mkl/lib/intel64/libmkl_core.a 
/SOFT/ics_2013.1.046/composer_xe_2013_sp1.2.144/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.a
  -Wl,--end-group -lm -lpthread

SCALAPACK_LIBS=-Wl,--start-group  
/SOFT/ics_2013.1.046/composer_xe_2013_sp1.2.144/mkl/lib/intel64/libmkl_scalapack_lp64.a
 
/SOFT/ics_2013.1.046/composer_xe_2013_sp1.2.144/mkl/lib/intel64/libmkl_intel_lp64.a
 
/SOFT/ics_2013.1.046/composer_xe_2013_sp1.2.144/mkl/lib/intel64/libmkl_sequential.a
 /SOFT/ics_2013.1.046/composer_xe_2013_sp1.2.144/mkl/lib/intel64/libmkl_core.a 
-lm -lpthread  -Wl,--end-group

#COMP_LIBS=libsiestaLAPACK.a


INCFLAGS += 
-I/UHOME/joshi.dcy2014/SOFTWARE/SIESTA/INTEL/Parrallel/TBTRANS/tbtrans_18-01-2018/Docs/build/netcdf/4.4.1.1/include
LDFLAGS += 
-L/UHOME/joshi.dcy2014/SOFTWARE/SIESTA/INTEL/Parrallel/TBTRANS/tbtrans_18-01-2018/Docs/build/zlib/1.2.8/lib
 
-Wl,-rpath=/UHOME/joshi.dcy2014/SOFTWARE/SIESTA/INTEL/Parrallel/TBTRANS/tbtrans_18-01-2018/Docs/build/zlib/1.2.8/lib
LDFLAGS += 
-L/UHOME/joshi.dcy2014/SOFTWARE/SIESTA/INTEL/Parrallel/TBTRANS/tbtrans_18-01-2018/Docs/build/hdf5/1.8.16/lib
 
-Wl,-rpath=/UHOME/joshi.dcy2014/SOFTWARE/SIESTA/INTEL/Parrallel/TBTRANS/tbtrans_18-01-2018/Docs/build/hdf5/1.8.16/lib
LDFLAGS += 
-L/UHOME/joshi.dcy2014/SOFTWARE/SIESTA/INTEL/Parrallel/TBTRANS/tbtrans_18-01-2018/Docs/build/netcdf/4.4.1.1/lib
 
-Wl,-rpath=/UHOME/joshi.dcy2014/SOFTWARE/SIESTA/INTEL/Parrallel/TBTRANS/tbtrans_18-01-2018/Docs/build/netcdf/4.4.1.1/lib
LIBS += -lnetcdff -lnetcdf -lhdf5_hl -lhdf5 -lz
COMP_LIBS += libncdf.a libfdict.a
FPPFLAGS += -DCDF -DNCDF -DNCDF_4


LIBS=$(SCALAPACK_LIBS) $(BLACS_LIBS) $(LAPACK_LIBS) $(BLAS_LIBS) 

#SIESTA needs an F90 interface to MPI
#This will give you SIESTA's own implementation
#If your compiler vendor offers an alternative, you may change
#to it here.
MPI_INTERFACE=libmpi_f90.a
MPI_INCLUDE=.

#Dependency rules are created by autoconf according to whether
#discrete preprocessing is necessary or not.

.F.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_fixed_F)  $<
.F90.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_free_F90) $<
.f.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_fixed_f)  $<
.f90.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_free_f90)  $<

Re: [SIESTA-L] slow performance of TBTrans software in workstation with gcc compiler

[Ankita Joshi]

Dear Nick,I have parallel version of TBTrans 4.1 beta 3 installed in my 
workstation as well as cluster. I found a huge difference in the calculation in 
terms of CPU time when running calculations in workstation and cluster with 
same node. In workstation, the tbtrans is installed using gcc compiler and job 
finished in 8 days while in cluster, the same job finished in 6 hours when 
using intel compiler. I just want to know why it is so? And also, how to how 
get similar performance in workstation as in case of cluster?Thanks and 
Regards,Ankita > > >  > 

Re: [SIESTA-L] Problem restarting transiesta job

[Ankita Joshi]

> Dear all,> > I am facing problem in restarting a transiesta job. The last few 
> lines of my output file are: * WELCOME TO TRANSIESTA * 
> ***ts-Vha: -0.54939E-01 eVCreated the TranSIESTA H,S 
> sparsity pattern:  nrows_g=9048 nrows=9048 sparsity=.0291 nnzs=2378948, refcount: 1>Created the 
> TranSIESTA global update sparsity pattern:  sparsity for geom step 0)) nrows_g=9048 nrows=9048 sparsity=.0178 
> nnzs=1455804, refcount: 2>transiesta: Determining an optimal tri-matrix 
> using: atom+Lefttransiesta: Established a near-optimal partition for the 
> tri-diagonal matrix.BTD partitions (6): [ 1508, 1508, 1508, 1508, 1508, 1508 
> ]transiesta: Matrix elements in tri / full: 36385024 / 81866304transiesta: 
> mem of electrodes (static): 277.60MBtransiesta: mem of global update arrays 
> (static): 58.51MBtransiesta: mem of tri-diagonal matrices: 
> 1110.38MBtransiesta: Total memory usage: 1446.49MBtra
 nsiesta:

[SIESTA-L] Failed to generate .nc file in running tbtrans calculation

[Ankita Joshi]

Dear siesta users,I am using parallel version of tbtrans with netcdf4 support 
for running my calculations. Although there is no error in running calculation 
but I found that .nc file is missing. I am not able to understand this and 
thus, attaching the input/output files and also, the arch.make file. Could 
anyone please help me in finding out the error?Thanks and Regards,Ankita> > > > 
> > > > >  > >  > > >  > 


device.fdf
Description: application/vnd.fdf
# 
# Copyright (C) 1996-2016   The SIESTA group
#  This file is distributed under the terms of the
#  GNU General Public License: see COPYING in the top directory
#  or http://www.gnu.org/copyleft/gpl.txt.
# See Docs/Contributors.txt for a list of contributors.
#
.SUFFIXES:
.SUFFIXES: .f .F .o .a .f90 .F90

SIESTA_ARCH=x86_64-unknown-linux-gnu--Gfortran

OPENMPI_HOME=/usr/lib64/openmpi
FPP=
FPP_OUTPUT= 
FC=${OPENMPI_HOME}/bin/mpif90
RANLIB=echo

CC = gcc
FPP = $(FC) -E -P -x c
FC = gfortran
FC_SERIAL = gfortran

SYS=nag

SP_KIND=4
DP_KIND=8
KINDS=$(SP_KIND) $(DP_KIND)

# Add any other sensible compilation flags here
FFLAGS=-g -O2

FPPFLAGS= -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DCDF -DGRID_DP -DPHI_GRID_SP
LDFLAGS= -L${OPENMPI_HOME}/lib -L/usr/lib64 -L/usr/lib64/gfortran/modules

ARFLAGS_EXTRA=

FCFLAGS_fixed_f=
FCFLAGS_free_f90=
FPPFLAGS_fixed_F=
FPPFLAGS_free_F90=

INCFLAGS=-I/usr/include -I. -I/usr/include/openmpi-x86_64 
-I/usr/lib64/gfortran/modules
BLAS_LIBS=-lblas
LAPACK_LIBS=/usr/lib64/liblapack.a
BLACS_LIBS=
SCALAPACK_LIBS=-lscalapack

COMP_LIBS += libsiestaLAPACK.a 

LDFLAGS =

LIBS = $(COMP_LIBS)

NETCDF_LIBS=-lnetcdff -lnetcdf
NETCDF_INTERFACE=libnetcdf_f90.a

LIBS= $(NETCDF_LIBS) -lpthread $(SCALAPACK_LIBS) $(BLACS_LIBS) $(LAPACK_LIBS) 
$(BLAS_LIBS)

#SIESTA needs an F90 interface to MPI
#This will give you SIESTA's own implementation
#If your compiler vendor offers an alternative, you may change
#to it here.
MPI_INTERFACE=libmpi_f90.a
MPI_INCLUDE=.

INCFLAGS += 
-I/home/ankita/SOFTWARE/SIESTA-4.1/TBTRANS/TBTRANS_PARALLEL_WITH_NETCDF4/NETCDF4/build/netcdf/4.4.0/include
LDFLAGS += 
-L/home/ankita/SOFTWARE/SIESTA-4.1/TBTRANS/TBTRANS_PARALLEL_WITH_NETCDF4/NETCDF4/build/zlib/1.2.8/lib
 
-Wl,-rpath=/home/ankita/SOFTWARE/SIESTA-4.1/TBTRANS/TBTRANS_PARALLEL_WITH_NETCDF4/NETCDF4/build/zlib/1.2.8/lib
LDFLAGS += 
-L/home/ankita/SOFTWARE/SIESTA-4.1/TBTRANS/TBTRANS_PARALLEL_WITH_NETCDF4/NETCDF4/build/hdf5/1.8.16/lib
 
-Wl,-rpath=/home/ankita/SOFTWARE/SIESTA-4.1/TBTRANS/TBTRANS_PARALLEL_WITH_NETCDF4/NETCDF4/build/hdf5/1.8.16/lib
LDFLAGS += 
-L/home/ankita/SOFTWARE/SIESTA-4.1/TBTRANS/TBTRANS_PARALLEL_WITH_NETCDF4/NETCDF4/build/netcdf/4.4.0/lib
 
-Wl,-rpath=/home/ankita/SOFTWARE/SIESTA-4.1/TBTRANS/TBTRANS_PARALLEL_WITH_NETCDF4/NETCDF4/build/netcdf/4.4.0/lib
LIBS += -lnetcdff -lnetcdf -lhdf5_hl -lhdf5 -lz
COMP_LIBS += libncdf.a libfdict.a
FPPFLAGS += -DCDF -DNCDF -DNCDF_4

#Dependency rules are created by autoconf according to whether
#discrete preprocessing is necessary or not.
.F.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_fixed_F)  $< 
.F90.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_free_F90) $< 
.f.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_fixed_f)  $<
.f90.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_free_f90)  $<

TBtrans Version: siesta-4.1--625
Architecture  : x86_64-unknown-linux-gnu--Gfortran
Compiler flags: /usr/lib64/openmpi/bin/mpif90 -g -O2
PP flags  : -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DCDF -DGRID_DP 
-DPHI_GRID_SP -DCDF -DN1 -DNCDF_4 -DTBTRANS
Libraries : -lnetcdff -lnetcdf -lpthread -lscalapack  
/usr/lib64/liblapack.a -lblas -lnettcdff -lnetcdf -lhdf5_hl -lhdf5 -lz
PARALLEL version
NetCDF support
NetCDF-4 support

* Running on 4 nodes in parallel
>> Start of run:  29-SEP-2017  11:27:58

    
   *  WELCOME TO TBtrans  * 
    

reinit: Reading from standard input
** Dump of input data file 
SolutionMethodTransiesta
# ---
# Name and Label
# ---
SystemName  device
SystemLabel device
# ---
# Lattice
# ---
LatticeConstant 1.00 Ang
%block LatticeVectors
10.00  0.00  0.00
 0.00 18.613506  0.00
 0.00  0.00 21.312900
%endblock LatticeVectors
# ---
# Species and Atoms
# ---
NumberOfSpecies2
NumberOfAtoms100
%block ChemicalSpeciesLabel
  1   1  H
  2   6  C

Re: [SIESTA-L] parallel installation of netcdf4

[Ankita Joshi]

Dear Nick,Thanks for your suggestion and I will do the same. As far as parallel 
version of netcdf4 is concerned, I needed this for running tbtrans in parallel. 
Could you please that if there be huge difference (in terms of computational 
time) in running calculations using serial or parallel version of 
tbtrans?Thanks and Regards,AnkitaOn 28/09/17, Nick Papior  
<nickpap...@gmail.com> wrote:> Please note that there is no need to install the 
parallel version of netcdf4. It isn't required, in fact it will probably not 
make a huge difference.> > Secondly, you should use the script shipped with 
siesta-4.1-b3, not the one you linked. It contains the latest updates.> > > So 
my suggestion, stick with the serial netcdf4 version.> > > 2017-09-26 16:47 
GMT+02:00 Ankita Joshi <joshi.dcy2...@iitr.ac.in>:> > > Dear Nick,> > > > > > I 
am facing difficulty in installing the parallel version of netcdf4. From the 
link below, I have installed the serial version of netcdf4.> > > > > > 
https://www.
 mail-arc

[SIESTA-L] parallel installation of netcdf4

[Ankita Joshi]

Dear Nick,I am facing difficulty in installing the parallel version of netcdf4. 
From the link below, I have installed the serial version of 
netcdf4.https://www.mail-archive.com/siesta-l@uam.es/msg09275.htmlCould you 
please tell, how to install the parallel version by modifying the script given 
in the above link?Thanks and regards,Ankita

Re: [SIESTA-L] Problem in transiesta run

[Ankita Joshi]

Dear Nick,Thanks..I will follow these steps...Regards,AnkitaOn 23/09/17, Nick 
Papior  <nickpap...@gmail.com> wrote:> From the provided information it is hard 
for us to pin down the problem.Could you please follow these steps:> > 
https://answers.launchpad.net/siesta/+faq/2779> > > > such that we can figure 
out what has gone wrong?> > > > 2017-09-20 15:20 GMT+02:00 Ankita Joshi 
<joshi.dcy2...@iitr.ac.in>:> > > > > > Dear SIESTA users,> > > > > I am using 
SIESTA version 4.0. I am getting the following error in the end of the output 
file for transiesta run. > > > > > > netCDF error: NetCDF: Invalid argument> > 
Stopping Program from Node: 0> > 
--> > 
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD> > with 
errorcode 1.> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI 
processes.> > You may or may not see output from other processes, depending on> 
> exactly when Open MPI kills them.> > --
 

[SIESTA-L] Parallel version of TBTrans with Netcdf4 support

[Ankita Joshi]

Dear Siesta users,I have serial version of TBtrans 4.1 beta 2 with NetCDF4 
support installed in my system. But I am unable to install its parallel 
version. Could anyone explain to me in detail about parallel installation of 
TBtrans with NetCDF4 support? Thanks RegardsAnkita> > > >  >  > 

[SIESTA-L] Problem in transiesta run

[Ankita Joshi]

> Dear SIESTA users,> I am using SIESTA version 4.0. I am getting the following 
> error in the end of the output file for transiesta run. netCDF error: NetCDF: 
> Invalid argumentStopping Program from Node: 
> 0--MPI_ABORT
>  was invoked on rank 0 in communicator MPI_COMM_WORLDwith errorcode 1.NOTE: 
> invoking MPI_ABORT causes Open MPI to kill all MPI processes.You may or may 
> not see output from other processes, depending onexactly when Open MPI kills 
> them.--I
>  think that the problem occur due to improper installation of transiesta as I 
> faced the problem during its installation.After installing siesta 
> (https://pelios.csx.cam.ac.uk/~mc321/siesta.html), I tried to install 
> Transiesta but got the error "make: *** No rule to make target 
> `libnetcdf_f90.a', needed by `transiesta'. Stop."Then, I searched the mailing 
> list and someone has suggested to commen
 t the li

Re: [SIESTA-L] SCF did not converge in maximum number of steps.

[Ankita Joshi]

Dear Siesta users,Does anyone know which version of openmpi is suitable for 
compilation of Siesta 4.1 beta 2. Also, how to compile tbtrans with 
openmpi?Thanks and RegardsAnkita> > > >  >  > 

Re: [SIESTA-L] Error found in transmission curve of (7,0)-CNT

[Ankita Joshi]

Dear Nick,

Thanks for your response.



Actually, I did not performed any calculation for the optimization of the 
electrodes and scattering region of (7,0)-CNT. I will briefly explain you how I 
performed the calculations.

Firstly, I have performed transiesta calculation for the electrodes in order to 
get .TSHS file. Secondly, I have performed transiesta calculation for the 
system consisting of 56 atoms each in electrode region and 28 atoms in the 
device region. Thirdly, I have done tbtrans calculation for this system at a 
bias voltage of 2 V. Then, I plotted transmission curve for this system.

Can you please tell me what additional steps I have to perform apart from the 
above mentioned steps.

Thanks






Ankita Joshi









On 07/07/17, Nick Papior  <nickpap...@gmail.com> wrote:

> It is not clear at all how you have converged your full system.
> 
> 1. The output of transiesta is just as important (if not more important) to 
> check for inconsistencies. Check that both the electrodes and the scattering 
> region have converged sufficiently, 
> 
> 
> 2. You are applying a bias across a semiconducting CNT which may be very 
> troubling indeed and may require additional checks. Possibly transiesta 
> cannot calculate this system due to the semiconducting character of the CNT. 
> 
> 
> 
> 3. Your fdf-flag:
> TS.Elecs.DM.Update none
> 
> I would probably change this from "none" to "cross-terms" in case you really 
> want to pursue this system. 
> 
> 
> 4. Please reconsider your choice of k-points (they won't give wrong result, 
> but try and figure out what is wrong with them...)
> 
> 
> 2017-07-05 7:47 GMT+02:00 Ankita Joshi <joshi.dcy2...@iitr.ac.in>:
> 
> > 
> > > Dear siesta users,
> > > 
> > > 
> > > 
> > > Using SIESTA 4.1 beta2 version, I have done tbtrans calculation at bias 
> > > voltage of 2.0 V for (7,0)-CNT . I expect symmetric tunnelling in 
> > > transmission curve, however, found asymmetric tunnelling. I could not 
> > > understand the reason behind this problem. I am attaching my input file, 
> > > output file and transmission curve for the same. Can somebody check and 
> > > let me know the error?
> > > 
> > > 
> > > 
> > > 
> > > 
> > 
> > > Thanks,
> > > Ankita Joshi
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > < /blockqu 
> > 
> 
> 
> 
> 
> 
> -- 
> Kind regards Nick
> 
> 
>  
>  
>

[SIESTA-L] Error found in transmission curve of (7,0)-CNT

[Ankita Joshi]

> Dear siesta users,> > > > Using SIESTA 4.1 beta2 version, I have done tbtrans 
> calculation at bias voltage of 2.0 V for (7,0)-CNT . I expect symmetric 
> tunnelling in transmission curve, however, found asymmetric tunnelling. I 
> could not understand the reason behind this problem. I am attaching my input 
> file, output file and transmission curve for the same. Can somebody check and 
> let me know the error?> > > > > > Thanks,> Ankita Joshi> > > > > > > >  > 


input.fdf
Description: application/vnd.fdf
TBtrans Version: siesta-4.1--625
Architecture  : unknown
Compiler flags: gfortran -O2 -fPIC -ftree-vectorize
PP flags  : -DFC_HAVE_ABORT  -DCDF -DNCDF -DNCDF_4 -DTBTRANS
Libraries : libsiestaLAPACK.a libsiestaBLAS.a  libncdf.a libfdict.a  
-lnetcdff -lnetcdf --lhdf5_hl -lhdf5 -lz
SERIAL version
NetCDF support
NetCDF-4 support

* Running in serial mode
>> Start of run:  20-JUN-2017  10:40:27

    
   *  WELCOME TO TBtrans  * 
    

reinit: Reading from standard input
** Dump of input data file 
SolutionMethodTransiesta
# ---
# Name and Label
# ---
SystemName  7c0-cnt
SystemLabel 7c0-cnt
# ---
# Lattice
# ---
LatticeConstant 1.00 Ang
%block LatticeVectors
15.483528  0.00  0.00
 0.00 15.483528  0.00
 0.00  0.00 25.575480
%endblock LatticeVectors
# ---
# Species and Atoms
# ---
NumberOfSpecies1
NumberOfAtoms168
%block ChemicalSpeciesLabel
  1   6  C
%endblock ChemicalSpeciesLabel
%block kgrid_Monkhorst_Pack
  2000.0
  0200.0
  0020.0
%endblock kgrid_Monkhorst_Pack
AtomicCoordinatesFormat Ang
AtomicCoorFormatOut Ang
# ---
# Atomic Coordinates
# ---
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
  8.3518640  5.0687418  0.7104300 1
  6.0323021  5.5981666  0.7104300 1
 10.2120082  6.5521572  0.7104300 1
  5.000  7.7417641  0.7104300 1
 10.2120082  8.9313710  0.7104300 1
  6.0323021  9.8853616  0.7104300 1
  8.3518640 10.4147865  0.7104300 1
  7.1316642  5.0687418  1.4208600 1
  9.4512261  5.5981666  1.4208600 1
  5.2715200  6.5521572  1.4208600 1
 10.4835282  7.7417641  1.4208600 1
  5.2715200  8.9313710  1.4208600 1
  9.4512261  9.8853616  1.4208600 1
  7.1316642 10.4147865  1.4208600 1
  7.1316642  5.0687418  2.8417200 1
  9.4512261  5.5981666  2.8417200 1
  5.2715200  6.5521572  2.8417200 1
 10.4835282  7.7417641  2.8417200 1
  5.2715200  8.9313710  2.8417200 1
  9.4512261  9.8853616  2.8417200 1
  7.1316642 10.4147865  2.8417200 1
  8.3518640  5.0687418  3.5521500 1
  6.0323021  5.5981666  3.5521500 1
 10.2120082  6.5521572  3.5521500 1
  5.000  7.7417641  3.5521500 1
 10.2120082  8.9313710  3.5521500 1
  6.0323021  9.8853616  3.5521500 1
  8.3518640 10.4147865  3.5521500 1
  8.3518640  5.0687418  4.9730100 1
  6.0323021  5.5981666  4.9730100 1
 10.2120082  6.5521572  4.9730100 1
  5.000  7.7417641  4.9730100 1
 10.2120082  8.9313710  4.9730100 1
  6.0323021  9.8853616  4.9730100 1
  8.3518640 10.4147865  4.9730100 1
  7.1316642  5.0687418  5.6834400 1
  9.4512261  5.5981666  5.6834400 1
  5.2715200  6.5521572  5.6834400 1
 10.4835282  7.7417641  5.6834400 1
  5.2715200  8.9313710  5.6834400 1
  9.4512261  9.8853616  5.6834400 1
  7.1316642 10.4147865  5.6834400 1
  7.1316642  5.0687418  7.1043000 1
  9.4512261  5.5981666  7.1043000 1
  5.2715200  6.5521572  7.1043000 1
 10.4835282

Re: [SIESTA-L] restarting tbtrans calculations

[Ankita Joshi]

Dear siesta users,I am using SIESTA 4.1 beta2 version. For my system, I want to 
restart tbtrans calculations. Does anyone know how to restart tbtrans 
calculations?Thanks,Ankita Joshi

[SIESTA-L] Compilation of parallel version of siesta-4.1beta2 with netcdf4 in workstation

[Ankita Joshi]

> > Dear Siesta users,> > I have serial version of SIESTA 4.1 beta2 with 
> > TranSIESTA and TBtrans modules installed in my workstation. So, I can 
> > submit a job with only one processor which takes lot of time. Does anyone 
> > know how to install the parallel version of SIESTA 4.1 beta2 with 
> > TranSIESTA and TBtrans modules ?Thanks in advance.Regards,Ankita Joshi> > > 
> > > 

[SIESTA-L] Compilation of version version of siesta-4.1beta2 with netcdf4 in workstation

[Ankita Joshi]

> > Dear Siesta users,> > I have serial version of SIESTA 4.1 beta2 with 
> > TranSIESTA and TBtrans modules installed in my workstation. So, I can 
> > submit a job with only one processor which takes lot of time. Does anyone 
> > know how to install the parallel version of SIESTA 4.1 beta2 with 
> > TranSIESTA and TBtrans modules ?Thanks in advance.Regards,Ankita Joshi> > > 
> > > 

[SIESTA-L] Compilation of TranSIESTA with OPENMPI

[Ankita Joshi]

Hi siesta users,I have siesta 4.1 beta 2 installed in my system. Does anyone 
know how to compile TRANSIESTA with OPENMPI for running calculations in 
parallel mode.Regards,Ankita Joshi

[SIESTA-L] conductance using transiesta

[Ankita Joshi]

Dear users,After tbtrans run, I have obtained .AVTRANS file for k-averaged 
transmission. But now, I want to obtain conductance for my system. Please give 
your comments.Thanks Ankita Joshi

[SIESTA-L] Regarding calculation of current using transiesta/tbtrans

[Ankita Joshi]

Dear users,I have run a tbtrans calculation to obtain current for a bias 
voltage of -0.5 eV and I got the results also. But since I am new to siesta, 
can somebody help me what is the value of current for the applied bias voltage 
of -0.5 eV. And, also how to get I-V curve? The output of the tbtrans 
calculation is as follow:Currents (ensure entire Fermi function window):Left -> 
Right, V [V] / I [A]: -.49 V / -.558331E-06 ALeft -> Right, V [V] / P [W]: 
-.49 V / -.139566E-06 WThanks,Ankita

[SIESTA-L] Request for .fdf files to reproduce the results

[Ankita Joshi]

Dear users,I want to reproduce the results from the paper "Density functional 
method for nonequilibrium electron transport". Could anyone provide me the .fdf 
files for initial geometry of electrode and scattering region of any system in 
the above paper?Regards,Ankita

[SIESTA-L] Siesta calcuations run with more number of processors

[Ankita Joshi]

Dear users,Does anyone know how to run SIESTA calculations with more than one 
processor in serial run ?Thanks,Ankita

[SIESTA-L] how to install Netcdf4 for compilation of tbtrans in siesta 4.1b2

[Ankita Joshi]

Dear SIESTA users,I want to compile tbtrans using netcdf4 in siesta 4.1b2. Can 
someone send me a link to install netcdf4 ?Thanks in advance,Ankita Joshi

[SIESTA-L] Error in the compilation of tbtrans with netcdf4

[Ankita Joshi]

F90:(.text+0xbdc6): undefined reference to `zgemm_'
m_tbt_proj.F90:(.text+0xc0e7): undefined reference to `zgerc_'
m_tbt_diag.o: In function `__m_tbt_diag_MOD_norm_eigenstate_kpt':
m_tbt_diag.F90:(.text+0x1ed): undefined reference to `zgemm_'
m_tbt_diag.o: In function `__m_tbt_diag_MOD_calc_eig_kpt':
m_tbt_diag.F90:(.text+0x7a3): undefined reference to `zhpgvd_'
m_tbt_diag.F90:(.text+0xb5d): undefined reference to `zhpgv_'
m_tbt_diag.F90:(.text+0xc33): undefined reference to `zhpgvd_'
m_tbt_diag.o: In function `__m_tbt_diag_MOD_calc_sqrt_s_kpt':
m_tbt_diag.F90:(.text+0x12cb): undefined reference to `zhpevd_'
m_tbt_diag.F90:(.text+0x17df): undefined reference to `zgemm_'
m_tbt_diag.F90:(.text+0x18a2): undefined reference to `zhpev_'
m_tbt_diag.F90:(.text+0x1b87): undefined reference to `zhpevd_'
m_tbt_diag.F90:(.text+0x1c77): undefined reference to `zgemm_'
m_tbt_diag.o: In function `__m_tbt_diag_MOD_norm_eigenstate_gamma':
m_tbt_diag.F90:(.text+0x1e9f): undefined reference to `dgemm_'
m_tbt_diag.o: In function `__m_tbt_diag_MOD_calc_eig_gamma':
m_tbt_diag.F90:(.text+0x241f): undefined reference to `dspgvd_'
m_tbt_diag.F90:(.text+0x2770): undefined reference to `dspgv_'
m_tbt_diag.F90:(.text+0x2837): undefined reference to `dspgvd_'
m_tbt_diag.o: In function `__m_tbt_diag_MOD_calc_sqrt_s_gamma':
m_tbt_diag.F90:(.text+0x2e55): undefined reference to `dspevd_'
m_tbt_diag.F90:(.text+0x3331): undefined reference to `dgemm_'
m_tbt_diag.F90:(.text+0x33e5): undefined reference to `dspev_'
m_tbt_diag.F90:(.text+0x36d7): undefined reference to `dspevd_'
m_tbt_diag.F90:(.text+0x37cf): undefined reference to `dgemm_'
collect2: error: ld returned 1 exit status
make: *** [tbtrans] Error 1

Regards,
Ankita Joshi

[SIESTA-L] Command for k-averaged transmission

[Ankita Joshi]

Hello SIESTA users,

I am using SIESTA 4.1 beta-2 and want to get k-averaged transmission for my 
system by using TBtrans module. I have tried several commands but I got 
k-resolved transmission instead of k-averaged transmission. Does anyone know 
suitable flag to be used in input file for obtaining k-averaged transmission?

Regards,
Ankita Joshi

Re: [SIESTA-L] GUI for TranSIESTA

[Ankita Joshi]

> 
> Dear All,
> 
> 

Can you suggest me a software to build two-probe systems so as to perform a 
TranSIESTA calculation?

Regards
Ankita 





> 
> 
>  
>

[SIESTA-L] Structure setup for transiesta calculations

[Ankita Joshi]

Dear All,

Hi. I am new to SIESTA and TRANSEISTA. I want to perform transport calculations 
with transiesta for the system in which carbon nanotube act as scattering 
region and graphene act as electrodes. Please anyone suggest how to start with 
the modelling of the structure. 

Thanks

Regards 
Ankita

[SIESTA-L] Transiesta error: No electrode found in compilation of .fdf file for scattering region

[Ankita Joshi]

 I am using siesta version (siesta-4.1-b2) for running transport calculations 
using TranSIESTA. I ran ../Examples/TranSiesta/Elec using transiesta and it 
worked fine. Then, I copied *.TSHS file in the directory 
../Examples/TranSiesta/Scat. But the compilation of Run.fdf in 
../Examples/TranSiesta/Scat resulted into the following error:
transiesta: *** No electrode names were found, default Left/Right are expected
Could not find electrode: Left
Could not find electrode: Left
Stopping Program from Node: 0
Stopping Program from Node: 0

Please suggest me.