This is more of an announcement or warning than a proper blog post:
Both FX8350 and FX8150 have trouble running the pspw module causing the calculation to lead to exploding structures:
http://www.nwchem-sw.org/index.php/Special:AWCforum/st/id1059/Issue_with_pspw_using_nwchem_6.3....html
My other nodes have no trouble running the job in question. Also, the issue was only found in nwchem 6.3 -- nwchem 6.1.1 worked fine. So it's not an FX83x50 related fault per se.
Again, see the post at the nwchem-sw.org site for more information.
Lindqvist - a blog about Linux and Science. Mostly.
25 November 2013
18 November 2013
530. Briefly: Adding a new entry to Default applications in Gnome 3. Example using Firefox
I'm tired of google chrome/chromium -- for some reason more and more websites are rendering incorrectly in it. Part of the reason is because I refuse to allow just any website to set cookies, but that can't explain all instances (e.g. I'm having major issues with any elsevier journals). I'm also tired of google in general, especially after having spent some time with google plus.
Anyway, I recently showed how to install firefox: http://verahill.blogspot.com.au/2013/11/528-briefly-setting-up-64-bit-pre-built.html
I'll show here to set it as a selectable application in the System Settings/Details
At the beginning the following selections are available:
The key to adding a new 'Default Application' is simply making sure that it appears in the MIME file type associations. And one way to do that is to create a .desktop file and use update-desktop-database to read it:
Once that's done we get the following:
You can then set up a shortcut launcher, e.g.
(you could of course just have it execute the command directly, but what's the challenge in that?)
Anyway, I recently showed how to install firefox: http://verahill.blogspot.com.au/2013/11/528-briefly-setting-up-64-bit-pre-built.html
I'll show here to set it as a selectable application in the System Settings/Details
At the beginning the following selections are available:
The key to adding a new 'Default Application' is simply making sure that it appears in the MIME file type associations. And one way to do that is to create a .desktop file and use update-desktop-database to read it:
sudo cp /usr/share/applications/iceweasel.desktop /usr/share/applications/firefox.desktop sudo sed -i 's/Iceweasel/Firefox/g' /usr/share/applications/firefox.desktop sudo sed -i 's/Exec=iceweasel/Exec=firefox25/g' /usr/share/applications/firefox.desktop sudo sed -i 's/Icon=iceweasel/Icon=firefox/g' /usr/share/applications/firefox.desktop sudo update-desktop-database
Once that's done we get the following:
12 November 2013
529. Briefly: Error Writing spool: NT_STATUS_DISK_FULL
I recently had trouble printing on a networked printer at work, where we use 'Papercut' to share printers -- basically you submit your job, give your credentials, then run over to a printer and release the job.
Anyway, I suddenly had issues printing:
I'm not entirely sure what fixed it, but here's what I did
lpstat showed a number of jobs that had been submitted to the printer, but couldn't be released:
me@beryllium:~/Downloads$ lpstat
global-mfp-1166 me 591872 Mon 11 Nov 2013 12:36:29 EST
global-mfp-1167 me 993280 Mon 11 Nov 2013 12:36:44 EST
global-mfp-1168 me 2014208 Mon 11 Nov 2013 12:36:59 EST
global-mfp-1169 me 871424 Mon 11 Nov 2013 12:37:17 EST
global-mfp-1170 me 573440 Mon 11 Nov 2013 12:37:31 EST
global-mfp-1171 me 1199104 Mon 11 Nov 2013 12:37:51 EST
global-mfp-1172 me 183296 Mon 11 Nov 2013 12:38:02 EST
global-mfp-1173 me 491520 Mon 11 Nov 2013 12:38:19 EST
global-mfp-1174 me 2035712 Mon 11 Nov 2013 12:38:38 EST
global-mfp-1175 me 2035712 Mon 11 Nov 2013 12:39:54 EST
global-mfp-1176 me 635904 Mon 11 Nov 2013 12:41:54 EST
global-mfp-1177 me 148480 Mon 11 Nov 2013 16:29:58 EST
I preceded to cancel all the jobs:
me@beryllium:~/Downloads$ cancel global-mfp-1166
me@beryllium:~/Downloads$ lpstat
global-mfp-1167 me 993280 Mon 11 Nov 2013 12:36:44 EST
global-mfp-1168 me 2014208 Mon 11 Nov 2013 12:36:59 EST
global-mfp-1169 me 871424 Mon 11 Nov 2013 12:37:17 EST
global-mfp-1170 me 573440 Mon 11 Nov 2013 12:37:31 EST
global-mfp-1171 me 1199104 Mon 11 Nov 2013 12:37:51 EST
global-mfp-1172 me 183296 Mon 11 Nov 2013 12:38:02 EST
global-mfp-1173 me 491520 Mon 11 Nov 2013 12:38:19 EST
global-mfp-1174 me 2035712 Mon 11 Nov 2013 12:38:38 EST
global-mfp-1175 me 2035712 Mon 11 Nov 2013 12:39:54 EST
global-mfp-1176 me 635904 Mon 11 Nov 2013 12:41:54 EST
global-mfp-1177 me 148480 Mon 11 Nov 2013 16:29:58 EST
me@beryllium:~/Downloads$ cancel global-mfp-1167
me@beryllium:~/Downloads$ cancel global-mfp-1168
me@beryllium:~/Downloads$ cancel global-mfp-1169
me@beryllium:~/Downloads$ cancel global-mfp-1170
me@beryllium:~/Downloads$ cancel global-mfp-1171
me@beryllium:~/Downloads$ cancel global-mfp-1172
me@beryllium:~/Downloads$ cancel global-mfp-1173
me@beryllium:~/Downloads$ cancel global-mfp-1174
me@beryllium:~/Downloads$ cancel global-mfp-1175
me@beryllium:~/Downloads$ cancel global-mfp-1176
me@beryllium:~/Downloads$ cancel global-mfp-1177
me@beryllium:~/Downloads$ lpstat
me@beryllium:~/Downloads$
That didn't remove the error message, however. Opening Printers in Gnome(3) showed that the printer with an issues was set to 'off'. Unlocking and changing it to 'on' resolved the issue.
07 November 2013
528. Briefly: Setting up 64 bit pre-built firefox (25) binaries on debian
/usr/local/lib is just a suggestion (and probably not a very good one).
Anyway, here's the quick and easy way to get set up with 64 bit firefox. Start it by calling firefox25
Anyway, here's the quick and easy way to get set up with 64 bit firefox. Start it by calling firefox25
mkdir ~/tmp cd ~/tmp wget ftp://ftp.mozilla.org/pub/firefox/releases/25.0/linux-x86_64/en-GB/firefox-25.0.tar.bz2 tar xvf firefox-25.0.tar.bz2 cd firefox/ sudo mkdir /usr/local/lib/firefox-25.0 sudo cp * -R /usr/local/lib/firefox-25.0 sudo ln -s /usr/local/lib/firefox-25.0/firefox /usr/bin/firefox25
527. Briefly: setting up thunderbird 24.1.0 on Debian (binaries)
Not much to say, other than that building thunderbird is a bit more complex these days than simply doing a configure/make/make install pass. For once I decided that rolling my own version wasn't worth it, and grabbed the pre-built binaries instead.
Here's a very brief description of how to get them set up:
Here's a very brief description of how to get them set up:
mkdir ~/tmp cd ~/tmp wget ftp://ftp.mozilla.org/pub/mozilla.org/thunderbird/releases/24.1.0/linux-x86_64/en-GB/thunderbird-24.1.0.tar.bz2 tar xvf thunderbird-24.1.0.tar.bz2 cd thunderbird/ sudo mkdir /usr/local/lib/thunderbird-24.1.0 sudo cp * -R /usr/local/lib/thunderbird-24.1.0 sudo rm /usr/local/bin/thunderbird sudo ln -s /usr/local/lib/thunderbird-24.1.0/thunderbird /usr/local/bin/thunderbird
04 November 2013
526. New release of NWChem 6.3 out (17th of October 2013)
There's recently a new release of nwchem 6.3 (release 2). As usual there's no public message, no release notes or anything that actually informs you as to whether there are critical bug fixes, new functionality or anything else.
The new version can be found here: http://www.nwchem-sw.org/download.php?f=Nwchem-6.3.revision2-src.2013-10-17.tar.gz
I'm not competent in telling you whether you should upgrade or not, but here's a list over the changed files:
In other words, there's been changes to the TDDFT module, to the dplot module, TCE etc.
Looking through the nwchem forum, I think the following posts may hint at what's been changed:
tddft: http://www.nwchem-sw.org/index.php/Special:AWCforum/st/id889/Possible_Bug_in_NWCHEM%3A_TD-B97.html
dplot: http://www.nwchem-sw.org/index.php/Special:AWCforum/st/id1013/Dplot_output_charge_density%2C_tot....html. The integrated (electron) density is printed now.
Not sure about the TCE though.
Here's the (almost fulle) diff -r output:
The new version can be found here: http://www.nwchem-sw.org/download.php?f=Nwchem-6.3.revision2-src.2013-10-17.tar.gz
I'm not competent in telling you whether you should upgrade or not, but here's a list over the changed files:
nwchem-6.3.revision2-src.2013-10-17/INSTALL nwchem-6.3.revision2-src.2013-10-17/src/config/makefile.h nwchem-6.3.revision2-src.2013-10-17/src/dplot/create_contour.F nwchem-6.3.revision2-src.2013-10-17/src/dplot/dplot_dump.F nwchem-6.3.revision2-src.2013-10-17/src/dplot/dplot.F nwchem-6.3.revision2-src.2013-10-17/src/dplot/dplot_input.F nwchem-6.3.revision2-src.2013-10-17/src/dplot/get_transden.F nwchem-6.3.revision2-src.2013-10-17/src/mcscf/detci/detci_spin.F nwchem-6.3.revision2-src.2013-10-17/src/nwdft/lr_tddft/tddft_analysis.F nwchem-6.3.revision2-src.2013-10-17/src/nwdft/lr_tddft/tddft_davidson.F nwchem-6.3.revision2-src.2013-10-17/src/nwdft/lr_tddft/tddft_init.F nwchem-6.3.revision2-src.2013-10-17/src/nwdft/lr_tddft/tddft_residual.F nwchem-6.3.revision2-src.2013-10-17/src/nwpw/nwpwlib/Parallel/Parallel-tcgmsg.F nwchem-6.3.revision2-src.2013-10-17/src/tce/tce_input.F nwchem-6.3.revision2-src.2013-10-17/src/tce/tce_mo2e_hybrid_2eorb_split.F nwchem-6.3.revision2-src.2013-10-17/src/tce/tce_mo2e_zones_4a_disk_ga_chop_N5.F nwchem-6.3.revision2-src.2013-10-17/src/tce/tce_mo2e_zones_4a_disk_ga_N5.F nwchem-6.3.revision2-src.2013-10-17/src/tools/GNUmakefile nwchem-6.3.revision2-src.2013-10-17/src/util/util_nwchem_version.F
In other words, there's been changes to the TDDFT module, to the dplot module, TCE etc.
Looking through the nwchem forum, I think the following posts may hint at what's been changed:
tddft: http://www.nwchem-sw.org/index.php/Special:AWCforum/st/id889/Possible_Bug_in_NWCHEM%3A_TD-B97.html
dplot: http://www.nwchem-sw.org/index.php/Special:AWCforum/st/id1013/Dplot_output_charge_density%2C_tot....html. The integrated (electron) density is printed now.
Not sure about the TCE though.
Here's the (almost fulle) diff -r output:
Only in nwchem-6.3-src.2013-05-28/QA/tests: dplot
diff -r nwchem-6.3-src.2013-05-28/src/config/makefile.h nwchem-6.3.revision2-src.2013-10-17/src/config/makefile.h
2c2
< # $Id: makefile.h 24201 2013-05-09 00:59:44Z edo $
---
> # $Id: makefile.h 24592 2013-09-24 18:49:32Z jhammond $
1171c1171
< GNUMAJOR=$(shell $(FC) -dM -E - < /dev/null | egrep __VERS | cut -c22)
---
> GNUMAJOR=$(shell $(FC) -dM -E - < /dev/null 2> /dev/null | egrep __VERS | cut -c22)
1173c1173
< GNUMINOR=$(shell $(FC) -dM -E - < /dev/null | egrep __VERS | cut -c24)
---
> GNUMINOR=$(shell $(FC) -dM -E - < /dev/null 2> /dev/null | egrep __VERS | cut -c24)
1305c1305
< GNUMAJOR=$(shell $(FC) -dM -E - < /dev/null | egrep __VERS | cut -c22)
---
> GNUMAJOR=$(shell $(FC) -dM -E - < /dev/null 2> /dev/null | egrep __VERS | cut -c22)
1307c1307
< GNUMINOR=$(shell $(FC) -dM -E - < /dev/null | egrep __VERS | cut -c24)
---
> GNUMINOR=$(shell $(FC) -dM -E - < /dev/null 2> /dev/null | egrep __VERS | cut -c24)
1532c1532
< GNUMAJOR=$(shell $(FC) -dM -E - < /dev/null | egrep __VERS | cut -c22)
---
> GNUMAJOR=$(shell $(FC) -dM -E - < /dev/null 2> /dev/null | egrep __VERS | cut -c22)
1534c1534
< GNUMINOR=$(shell $(FC) -dM -E - < /dev/null | egrep __VERS | cut -c24)
---
> GNUMINOR=$(shell $(FC) -dM -E - < /dev/null 2> /dev/null | egrep __VERS | cut -c24)
1697,1700c1697,1704
< ifdef USE_I4FLAGS
< ifeq ($(_FC),gfortran)
< #wrong FOPTIONS += -fdefault-integer-8
< else ifeq ($(_FC),crayftn)
---
> ifeq ($(_FC),gfortran)
> ifdef USE_I4FLAGS
> # FOPTIONS += -fdefault-integer-4
> else
> FOPTIONS += -fdefault-integer-8
> endif
> else ifeq ($(_FC),crayftn)
> ifdef USE_I4FLAGS
1702,1708c1706
< else
< FOPTIONS += -i4
< endif
< else
< ifeq ($(_FC),gfortran)
< FOPTIONS += -fdefault-integer-8
< else ifeq ($(_FC),crayftn)
---
> else
1710,1715c1708,1717
< else
< FOPTIONS += -i8
< endif
< endif
< DEFINES += -DEXT_INT
< MAKEFLAGS = -j 1 --no-print-directory
---
> endif
> else
> ifdef USE_I4FLAGS
> FOPTIONS += -i4
> else
> FOPTIONS += -i8
> endif
> endif
> DEFINES += -DEXT_INT
> MAKEFLAGS = -j 1 --no-print-directory
1954c1956
< GNUMAJOR=$(shell $(FC) -dM -E - < /dev/null | egrep __VERS | cut -c22)
---
> GNUMAJOR=$(shell $(FC) -dM -E - < /dev/null 2> /dev/null | egrep __VERS | cut -c22)
1956c1958
< GNUMINOR=$(shell $(FC) -dM -E - < /dev/null | egrep __VERS | cut -c24)
---
> GNUMINOR=$(shell $(FC) -dM -E - < /dev/null 2> /dev/null | egrep __VERS | cut -c24)
1969a1972,1974
> ifeq ($(GNU_GE_4_6),true)
> FOPTIMIZE += -march=native -mtune=native
> else
1974,1976d1978
< ifeq ($(GNU_GE_4_6),true)
< FOPTIMIZE += -march=native -mtune=native
< else
2198d2199
< EXPLICITF = TRUE
2211a2213
> EXPLICITF = TRUE
2224a2227
> EXPLICITF = TRUE
2247c2250,2251
< #CC = mpicc
---
> FC = mpixlf77_r
>
2248a2253
> CC = mpicc
2251,2253c2256,2258
< FOPTIONS += -g -funderscoring
< FOPTIMIZE += -O3 -ffast-math -Wuninitialized
< FOPTIMIZE += -O0 -g
---
> FOPTIONS += -g -funderscoring -Wuninitialized
> FOPTIMIZE += -O3 -ffast-math
> FDEBUG += -O1 -g
2262c2267,2281
< CORE_LIBS += -llapack -lblas
---
> CORE_LIBS += -llapack $(BLASOPT) -lblas
>
> # Here is an example for ALCF:
> # IBMCMP_ROOT=${IBM_MAIN_DIR}
> # BLAS_LIB=/soft/libraries/alcf/current/xl/BLAS/lib
> # LAPACK_LIB=/soft/libraries/alcf/current/xl/LAPACK/lib
> # ESSL_LIB=/soft/libraries/essl/current/essl/5.1/lib64
> # XLF_LIB=${IBMCMP_ROOT}/xlf/bg/14.1/bglib64
> # XLSMP_LIB=${IBMCMP_ROOT}/xlsmp/bg/3.1/bglib64
> # XLMASS_LIB=${IBMCMP_ROOT}/xlmass/bg/7.3/bglib64
> # MATH_LIBS="-L${XLMASS_LIB} -lmass -L${LAPACK_LIB} -llapack \
> -L${ESSL_LIB} -lesslsmpbg -L${XLF_LIB} -lxlf90_r \
> -L${XLSMP_LIB} -lxlsmp -lxlopt -lxlfmath -lxl \
> -Wl,--allow-multiple-definition"
> # Note that ESSL _requires_ USE_64TO32 on Blue Gene
2265,2266d2283
< FC = mpixlf77_r
< CC = mpixlc_r
2267a2285,2286
> EXPLICITF = TRUE
> CC = mpixlc_r
2274,2278d2292
< ifdef USE_I4FLAGS
< FOPTIONS = -qintsize=4
< else
< FOPTIONS = -qintsize=8
< endif
2280,2284c2294,2318
< FOPTIONS += -qEXTNAME -qxlf77=leadzero
< FOPTIONS += -qstrict -qthreaded -qnosave -g
< FOPTIMIZE += -O2 -qarch=qp -qtune=qp -qcache=auto -qunroll=auto -qfloat=rsqrt
< # FOPTIMIZE += -qhot=level=0
< FDEBUG = -O0
---
> ifdef USE_I4FLAGS
> FOPTIONS = -qintsize=4
> ifeq ($(BLAS_SIZE),8)
> @echo "You cannot use BLAS with 64b integers when"
> @echo "the compiler generates 32b integers (USE_I4FLAGS)!"
> @exit 1
> endif # BLAS_SIZE
> else
> FOPTIONS = -qintsize=8
> ifeq ($(BLAS_SIZE),4)
> ifneq ($(USE_64TO32),y)
> @echo "You cannot use BLAS with 32b integers when"
> @echo "the compiler generates 64b integers unless"
> @echo "you do the 64-to-32 conversion!"
> @exit 1
> endif # USE_64TO32
> endif # BLAS_SIZE
> endif # USE_I4FLAGS
>
> FDEBUG = -g -qstrict -O3
> FOPTIONS += -g -qEXTNAME -qxlf77=leadzero
> FOPTIONS += -qthreaded -qnosave # -qstrict
> # FOPTIMIZE += -g -O3 -qarch=qp -qtune=qp -qcache=auto -qunroll=auto -qfloat=rsqrt
> FOPTIMIZE += -O3 -qarch=qp -qtune=qp -qsimd=auto -qhot=level=1 -qprefetch -qunroll=yes #-qnoipa
> FOPTIMIZE += -qreport -qsource -qlistopt -qlist # verbose compiler output
2425a2460,2466
> ifeq ($(ARMCI_NETWORK),ARMCI)
> ifdef EXTERNAL_ARMCI_PATH
> CORE_LIBS += -L$(EXTERNAL_ARMCI_PATH)/lib -larmci
> else
> CORE_LIBS += -L$(NWCHEM_TOP)/src/tools/install/lib -larmci
> endif
> else
2426a2468
> endif
diff -r nwchem-6.3-src.2013-05-28/src/dplot/create_contour.F nwchem-6.3.revision2-src.2013-10-17/src/dplot/create_contour.F
4c4
< . no_of_spacings,
---
> . no_of_spacings,tol_rho,
7c7
< * $Id: create_contour.F 19697 2010-10-29 16:57:34Z d3y133 $
---
> * $Id: create_contour.F 24552 2013-08-31 21:23:45Z niri $
30a31
> double precision tol_rho
46d46
< Double Precision TOLL
247d246
< TOLL=1.D-15
257c256
<
---
> c
259,271c258,271
< T TOLL,AO_Bas_Han,g_Dns,
< & nbf_ao_mxnbf_ce,nAtom,1,1,1,
< U 1,ngrpp,nBF,mBF,.false.,1,
< & Dbl_mb(k_FMat),Dbl_mb(k_PMat),
< & Dbl_mb(k_BMat),0d0,
< & Dbl_mb(k_Scr1),0,0d0,Int_mb(k_ibf),
< & Int_mb(k_iniz),Int_mb(k_ifin),
< & Values(iOffg),0,
< & dbl_mb(irchi_atom), 0,
< & dbl_mb(k_rdat), int_mb(k_cetobfr),1d0,
< & 0, 0, .false. )
<
<
---
> T tol_rho,
> & AO_Bas_Han,
> & g_Dns,
> & nbf_ao_mxnbf_ce,
> & nAtom,
> & 1,1,1,
> U 1,ngrpp,nBF,mBF,.false.,1,
> & Dbl_mb(k_FMat),Dbl_mb(k_PMat),Dbl_mb(k_BMat),0d0,
> & Dbl_mb(k_Scr1),0,0d0,Int_mb(k_ibf),
> & Int_mb(k_iniz),Int_mb(k_ifin), Values(iOffg),0,
> & dbl_mb(irchi_atom),0,
> & dbl_mb(k_rdat),int_mb(k_cetobfr),100.d0,
> & 0, .false. )
> c
diff -r nwchem-6.3-src.2013-05-28/src/dplot/dplot_dump.F nwchem-6.3.revision2-src.2013-10-17/src/dplot/dplot_dump.F
3c3
< , natom,xyz,charge,volume,
---
> , natom,xyz,charge,volume,tol_rho,
17c17
< double precision spread(3),step(3),angle(3)
---
> double precision spread(3),step(3),angle(3),tol_rho
34,35c34,35
< Write(Out_Unit,*)Title
< Write(Out_Unit,*) 'Total Density'
---
> Write(Out_Unit,*)"Cube file generated by NWChem"
> Write(Out_Unit,*) Title
80c80,81
< if(lgaussian) then
---
> c
> if(lgaussian) then ! for cube files
85,86c86
< if(abs(values(i)).lt.1d-10)
< . values(i)=0d0
---
> if(abs(values(i)).lt.tol_rho) values(i)=0d0
113c113
< c $Id: dplot_dump.F 21176 2011-10-10 06:35:49Z d3y133 $
---
> c $Id: dplot_dump.F 24552 2013-08-31 21:23:45Z niri $
diff -r nwchem-6.3-src.2013-05-28/src/dplot/dplot.F nwchem-6.3.revision2-src.2013-10-17/src/dplot/dplot.F
3c3
< * $Id: dplot.F 24177 2013-05-03 20:42:30Z d3y133 $
---
> * $Id: dplot.F 24552 2013-08-31 21:23:45Z niri $
59a60
> double precision tol_rho
120a122,125
> c -- Read tol_rho
> if (.not. rtdb_get(rtdb, 'dplot:tol_rho', mt_dbl, 1,
> & tol_rho)) call errquit('dpinput:rtdbget failed',11, RTDB_ERR)
> c
498a504,505
> call int_init(rtdb,1,AO_Bas_Han)
> if (iproc.eq.0) write(luout,*) ' Root: ', iroot
500a508
> call int_terminate()
563c571
< . no_of_spacings,
---
> . no_of_spacings, tol_rho,
607c615
< , natom,dbl_mb(k_xyz),dbl_mb(k_charge),volume,
---
> , natom,dbl_mb(k_xyz),dbl_mb(k_charge),volume,tol_rho,
diff -r nwchem-6.3-src.2013-05-28/src/dplot/dplot_input.F nwchem-6.3.revision2-src.2013-10-17/src/dplot/dplot_input.F
3c3
< * $Id: dplot_input.F 22941 2012-09-30 02:37:23Z niri $
---
> * $Id: dplot_input.F 24552 2013-08-31 21:23:45Z niri $
22c22
< Parameter (Num_Dirs = 15)
---
> Parameter (Num_Dirs = 16)
40a41
> double precision tol_rho
45c46
< A 'dos',
---
> A 'dos','tol_rho',
61c62,63
< dodos =.false.
---
> dodos =.false.
> iroot = 1
103c105
< & 900, 964, 1997, 9999) ind
---
> & 900, 964, 1997, 1998, 9999) ind
162d163
< iroot = 0
252a254
> c
255a258
> c
258a262,269
> c
> 1998 continue
> tol_rho = 1d-15
> If (.not. inp_f(tol_rho))
> & Call ErrQuit('DPlot_Input: failed to read tol_rho',0,
> & INPUT_ERR)
> goto 10
> c
339a351,356
> *
> If (.not.rtdb_put(rtdb,'dplot:tol_rho',mt_dbl,
> & 1,tol_rho))
> & Call ErrQuit('DPlot_Input: rtdb_put failed - tol_rho',0,
> & RTDB_ERR)
> *
diff -r nwchem-6.3-src.2013-05-28/src/dplot/get_transden.F nwchem-6.3.revision2-src.2013-10-17/src/dplot/get_transden.F
4c4
< & g_movecs, g_dens)
---
> & g_movecs, g_tdens)
24c24
< integer basis ! AO basis set handle
---
> integer basis ! AO basis set handle
26c26
< integer g_dens(ipol) ! Number of AO basis functions
---
> integer g_tdens(ipol) ! Transition density matrix
36c36,37
< double precision r
---
> integer icntr,itmom
> double precision r,cntr(3),tmom(20)
54a56
> call ga_sync()
58a61
> c initialization
60c63
< call ga_zero(g_dens(i))
---
> call ga_zero(g_tdens(i))
61a65,70
> do icntr=1,3
> cntr(icntr)=0.0d0
> enddo
> do itmom=1,20
> tmom(itmom)=0.0d0
> enddo
77a87,91
> if (ipol.eq.1) nocc(2)=0
> if (ipol.eq.1) nmo(2)=0
> if (ipol.eq.1) nfc(2)=0
> if (ipol.eq.1) nfv(2)=0
> c
119c133
< open(unit=69,file=filename,form='formatted',
---
> open(unit=69,file=filename,form='formatted',
133,135c147,150
< read(69,*) r ! energy of root
< do i=1,ipol
< if (tda) then
---
> if (tda) then
> read(69,*) r ! energy of root
> read(69,*) r ! s2_save(n)
> do i=1,ipol
140c155,159
< else
---
> end do ! ipol
> else ! full tddft
> read(69,*) r ! energy of root
> read(69,*) r ! s2_save(n)
> do i=1,ipol
144a164,166
> end do ! ipol
> c
> do i=1,ipol
149,150c171,172
< end if ! tda
< end do ! ipol
---
> end do ! ipol
> end if ! tda
152c174,175
< close(unit=69,status='keep',err=1002) ! file
---
> close(unit=69,status='keep',err=1002) ! file
> ok = 1
153a177,178
> c
> call ga_brdcst(Msg_Vec_Stat+MSGINT, ok, inntsize, 0)
159c184
< do i=1,ipol
---
> do i=1,ipol
162c187
< enddo
---
> enddo
169c194,195
< call ga_copy(g_temp(i),g_dens(i))
---
> call multipole_density(basis,cntr,3,g_temp(i),tmom,20) ! transition moments
> call ga_copy(g_temp(i),g_tdens(i))
174c200,203
< call tddft_transfm(iroot,g_y,g_movecs,nbf_ao,nocc,nmo,
---
> do i = 1,ipol
> call ga_zero(g_temp(i))
> end do
> call tddft_transfm(iroot,g_y,g_movecs,nbf_ao,nocc,nmo,
177,180c206,210
< c accumulate the Y component of the transition density matrix
< do i = 1,ipol
< call ga_add(1.d0,g_dens(i),1.d0,g_temp(i),g_dens(i))
< end do
---
> c accumulate the Y component of the transition density matrix
> do i = 1,ipol
> call multipole_density(basis,cntr,3,g_temp(i),tmom,20) ! transition moments
> call ga_add(1.d0,g_tdens(i),1.d0,g_temp(i),g_tdens(i))
> end do
182a213,229
> if (ipol.eq.1) then
> do i=1,20
> tmom(i)=tmom(i)*dsqrt(2.0d0)
> enddo
> end if
> c
> if (ga_nodeid().eq.0) then
> write(luout,*) " *** tmom(2)***: ", tmom(2)
> write(luout,*) " *** tmom(3)***: ", tmom(3)
> write(luout,*) " *** tmom(4)***: ", tmom(4)
> end if
> c
> c symmetrize the transition density matrix
> do i = 1,ipol
> call ga_symmetrize(g_tdens(i))
> enddo
> c
186c233
< Call GA_dAdd(1.d0,g_dens(1),1.d0,g_dens(2),g_dens(1))
---
> Call GA_dAdd(1.d0,g_tdens(1),1.d0,g_tdens(2),g_tdens(1))
188c235
< Call GA_dAdd(1.d0,g_dens(1),-1.d0,g_dens(2),g_dens(1))
---
> Call GA_dAdd(1.d0,g_tdens(1),-1.d0,g_tdens(2),g_tdens(1))
191c238
< Call GA_Copy(g_dens(2),g_dens(1))
---
> Call GA_Copy(g_tdens(2),g_tdens(1))
194a242
> c cleanup
diff -r nwchem-6.3-src.2013-05-28/src/mcscf/detci/detci_spin.F nwchem-6.3.revision2-src.2013-10-17/src/mcscf/detci/detci_spin.F
12c12
< * $Id: detci_spin.F 23708 2013-03-08 21:13:06Z bert $
---
> * $Id: detci_spin.F 24317 2013-06-12 16:58:14Z d3y133 $
162c162,163
< call ga_access(g_civec, blo, bhi, alo, ahi, k_xxci, bdim)
---
> if (bhi.gt.0.and.ahi.gt.0) then
> call ga_access(g_civec, blo, bhi, alo, ahi, k_xxci, bdim)
164c165
< c Allocate scatter data block and pointer blocks
---
> c Allocate scatter data block and pointer blocks
166,203c167,206
< scat_dim = 40000
< if (.not.ma_push_get(MT_DBL, scat_dim, 'detci:lowdin',
< $ l_xa, k_xa))
< $ call errquit('detci: cannot allocate xa lowdin',0, MA_ERR)
< if (.not.ma_push_get(MT_INT, scat_dim, 'detci:lowdin',
< $ l_ib, k_ib))
< $ call errquit('detci: cannot allocate ib lowdin',0, MA_ERR)
< if (.not.ma_push_get(MT_INT, scat_dim, 'detci:lowdin',
< $ l_ia, k_ia))
< $ call errquit('detci: cannot allocate ia lowdin',0, MA_ERR)
< do istra = alo, ahi
< call ifill((detci_maxorb*detci_maxorb),0,eij,1)
< call ifill((detci_maxorb*detci_maxorb),0,pij,1)
< do iex=1,nexa
< eij(exa(6,iex,istra),exa(5,iex,istra)) = exa(1,iex,istra)
< pij(exa(6,iex,istra),exa(5,iex,istra)) = exa(4,iex,istra)
< enddo
< offset=(istra-alo)*bdim-blo
< do istrb = blo, bhi
< val = -dbl_mb(k_xxci+offset+istrb)
< if (dabs(val).gt.1.0d-14) then
< do iex=1,nexb
< iib = exb(5,iex,istrb)
< jjb = exb(6,iex,istrb)
< if ((eij(iib,jjb).ne.0).and.(pij(iib,jjb).ne.0)) then
< jstrb = exb(1,iex,istrb)
< jstra = eij(iib,jjb)
< xx = val*pij(iib,jjb)*exb(4,iex,istrb)
< if (dabs(xx).gt.1.0d-14) then
< isc=isc+1
< dbl_mb(k_xa+isc-1)=xx
< int_mb(k_ib+isc-1)=jstrb
< int_mb(k_ia+isc-1)=jstra
< if (isc.eq.scat_dim) then
< call ga_scatter_acc(g_pvec,dbl_mb(k_xa),
< & int_mb(k_ib),int_mb(k_ia),isc,1.0d0)
< isc=0
< endif
---
> scat_dim = 40000
> if (.not.ma_push_get(MT_DBL, scat_dim, 'detci:lowdin',
> $ l_xa, k_xa))
> $ call errquit('detci: cannot allocate xa lowdin',0, MA_ERR)
> if (.not.ma_push_get(MT_INT, scat_dim, 'detci:lowdin',
> $ l_ib, k_ib))
> $ call errquit('detci: cannot allocate ib lowdin',0, MA_ERR)
> if (.not.ma_push_get(MT_INT, scat_dim, 'detci:lowdin',
> $ l_ia, k_ia))
> $ call errquit('detci: cannot allocate ia lowdin',0, MA_ERR)
> do istra = alo, ahi
> call ifill((detci_maxorb*detci_maxorb),0,eij,1)
> call ifill((detci_maxorb*detci_maxorb),0,pij,1)
> do iex=1,nexa
> eij(exa(6,iex,istra),exa(5,iex,istra)) = exa(1,iex,istra)
> pij(exa(6,iex,istra),exa(5,iex,istra)) = exa(4,iex,istra)
> enddo
> offset=(istra-alo)*bdim-blo
> do istrb = blo, bhi
> val = -dbl_mb(k_xxci+offset+istrb)
> if (dabs(val).gt.1.0d-14) then
> do iex=1,nexb
> iib = exb(5,iex,istrb)
> jjb = exb(6,iex,istrb)
> if ((eij(iib,jjb).ne.0).and.(pij(iib,jjb).ne.0))
> & then
> jstrb = exb(1,iex,istrb)
> jstra = eij(iib,jjb)
> xx = val*pij(iib,jjb)*exb(4,iex,istrb)
> if (dabs(xx).gt.1.0d-14) then
> isc=isc+1
> dbl_mb(k_xa+isc-1)=xx
> int_mb(k_ib+isc-1)=jstrb
> int_mb(k_ia+isc-1)=jstra
> if (isc.eq.scat_dim) then
> call ga_scatter_acc(g_pvec,dbl_mb(k_xa),
> & int_mb(k_ib),int_mb(k_ia),isc,1.0d0)
> isc=0
> endif
> endif
205,210c208,212
< endif
< enddo
< endif
< enddo
< enddo
< if (isc.gt.0) call ga_scatter_acc(g_pvec,dbl_mb(k_xa),
---
> enddo
> endif
> enddo
> enddo
> if (isc.gt.0) call ga_scatter_acc(g_pvec,dbl_mb(k_xa),
212c214,221
< call ga_release(g_civec, blo, bhi, alo, ahi)
---
> call ga_release(g_civec, blo, bhi, alo, ahi)
> if (.not.ma_pop_stack(l_ia))
> $ call errquit('cannot pop stack ia detci:lowdin',0, MA_ERR)
> if (.not.ma_pop_stack(l_ib))
> $ call errquit('cannot pop stack ib detci:lowdin',0, MA_ERR)
> if (.not.ma_pop_stack(l_xa))
> $ call errquit('cannot pop stack xa detci:lowdin',0, MA_ERR)
> endif
214,219d222
< if (.not.ma_pop_stack(l_ia))
< $ call errquit('cannot pop stack ia detci:lowdin',0, MA_ERR)
< if (.not.ma_pop_stack(l_ib))
< $ call errquit('cannot pop stack ib detci:lowdin',0, MA_ERR)
< if (.not.ma_pop_stack(l_xa))
< $ call errquit('cannot pop stack xa detci:lowdin',0, MA_ERR)
diff -r nwchem-6.3-src.2013-05-28/src/nwdft/lr_tddft/tddft_analysis.F nwchem-6.3.revision2-src.2013-10-17/src/nwdft/lr_tddft/tddft_analysis.F
6c6
< c $Id: tddft_analysis.F 24091 2013-04-17 17:22:55Z bert $
---
> c $Id: tddft_analysis.F 24553 2013-08-31 21:27:02Z niri $
179a180,182
> double precision s2_save(nroots)
> logical lstores2
> double precision s2_tmp(nroots)
219c222
< c CI Vectors file
---
> c CI Vectors file
222a226,239
> if (lcivecs) then
> do n=1,nroots
> if (ipol.eq.2) then ! unrestricted
> s2_save(n) = 0.0d0
> s2_tmp(n) = 0.0d0
> elseif (singlet) then ! restricted singlets
> s2_save(n) = 0.0d0
> s2_tmp(n) = 0.0d0
> elseif (triplet) then ! restricted triplets
> s2_save(n) = 2.0d0
> s2_tmp(n) = 2.0d0
> endif
> enddo
> endif
459,494d475
< c --------------------
< c Solution vector file
< c --------------------
< c
< if (.not.rtdb_cget(rtdb,'tddft:civecs',1,fn_civecs))
< 1 call errquit('tddft_analysis: failed to read vector',0)
< c
< len_fn_civecs = inp_strlen(fn_civecs)
< if (singlet) fn_civecs=fn_civecs(1:len_fn_civecs)//"_singlet"
< if (triplet) fn_civecs=fn_civecs(1:len_fn_civecs)//"_triplet"
< c
< if (nodezero.and.lcivecs) then
< write(luout,*) "fn_civecs: ",fn_civecs
< call util_file_name_resolve(fn_civecs, .false.)
< open(unit=69,file=fn_civecs,form='formatted',status='unknown')
< write(LuOut,2010) fn_civecs
< rewind(69)
< write(69,*) tda
< write(69,*) ipol
< write(69,*) nroots
< if (ipol.eq.1) nocc(2) = 0
< write(69,*) nocc(1),nocc(2)
< if (ipol.eq.1) nmo(2) = 0
< write(69,*) nmo(1),nmo(2)
< if (ipol.eq.1) nfc(2) = 0
< write(69,*) nfc(1),nfc(2)
< if (ipol.eq.1) nfv(2) = 0
< write(69,*) nfv(1),nfv(2)
< if (ipol.eq.1) nov(2) = 0
< write(69,*) nov(1),nov(2)
< write(69,*)
< endif ! nodezero
< c
< 2000 format(/,2x,'No CI vector file is created')
< 2010 format(/,2x,'CI vectors are stored in ',a32)
< c
517,530d497
< c Write out solution vectors: X (Y=0 in TDA)
< c
< if (nodezero.and.lcivecs) then
< do n=1,nroots
< write(69,*)apbval(n) ! energy of the root
< do i=1,ipol
< do m=1,nov(i)
< call ga_get(g_x(i),m,m,n,n,r,1)
< write(69,*) r
< enddo ! nov
< enddo ! ipol
< enddo ! nroots
< endif ! nodezero and lcivecs
< c
557,578d523
< c g_x = X+Y and g_y = X-Y
< c Write out vectors: X+Y and X-Y
< c
< if (nodezero.and.lcivecs) then
< do n=1,nroots
< write(69,*)apbval(n) ! energy of the root
< do i=1,ipol
< do m=1,nov(i)
< call ga_get(g_x(i),m,m,n,n,r,1) ! X vectors
< write(69,*) r
< enddo ! nov
< enddo ! ipol
< c
< do i=1,ipol
< do m=1,nov(i)
< call ga_get(g_y(i),m,m,n,n,r,1) ! Y vectors
< write(69,*) r
< enddo ! nov
< enddo ! ipol
< enddo ! nroots
< endif ! nodezero or lcivecs
< c
588,589d532
< if (nodezero.and.lcivecs) close(unit=69)
< c
652,653c595
<
<
---
> c
877a820
> if (lcivecs) s2_save(n) = s2
1662a1606,1730
> c
> c ----------------------------------------------------------------------
> c Store the <S2> value for the first cycle of a TDDFT
> c optimization in the RTDB. This will allow us to use it as a reference
> c for all optimization cycles.
> c ----------------------------------------------------------------------
> c
> if (lcivecs) then
> lstores2 = .false.
> c Check if <S2> is already in the RTDB. If it is, we don't do anything
> c else. Otherwise, we write s2_save to the RTDB. This only happens if
> c tddft_grad:s2 doesn't exist.
> if (.not.rtdb_get(rtdb,'tddft_grad:s2',mt_dbl,nroots,s2_tmp))
> 1 lstores2 = .true.
> if (lstores2) then
> if (.not.rtdb_put(rtdb,'tddft_grad:s2',mt_dbl,nroots,s2_save))
> 1 call errquit('tddft_analysis: failed to store s2', 0,
> 2 RTDB_ERR)
> endif
> endif
> c
> c ---------------------------
> c Handle solution vector file
> c ---------------------------
> c
> c On top of what was present originally for storing
> c the excited state information, we also need <S2> for unrestricted
> c calculations. This is required because we store every state and
> c it is possible that the states reorder. We can't use the character
> c of singlet and triplet states to identify states since they can be
> c similar.
> c
> if (.not.rtdb_cget(rtdb,'tddft:civecs',1,fn_civecs))
> 1 call errquit('tddft_analysis: failed to read vector',0,
> 2 RTDB_ERR)
> c
> len_fn_civecs = inp_strlen(fn_civecs)
> if (singlet) fn_civecs=fn_civecs(1:len_fn_civecs)//"_singlet"
> if (triplet) fn_civecs=fn_civecs(1:len_fn_civecs)//"_triplet"
> c
> if (nodezero.and.lcivecs) then
> write(luout,*) "fn_civecs: ",fn_civecs
> call util_file_name_resolve(fn_civecs, .false.)
> open(unit=69,file=fn_civecs,form='formatted',status='unknown')
> write(LuOut,2010) fn_civecs
> rewind(69)
> write(69,*) tda
> write(69,*) ipol
> write(69,*) nroots
> if (ipol.eq.1) nocc(2) = 0
> write(69,*) nocc(1),nocc(2)
> if (ipol.eq.1) nmo(2) = 0
> write(69,*) nmo(1),nmo(2)
> if (ipol.eq.1) nfc(2) = 0
> write(69,*) nfc(1),nfc(2)
> if (ipol.eq.1) nfv(2) = 0
> write(69,*) nfv(1),nfv(2)
> if (ipol.eq.1) nov(2) = 0
> write(69,*) nov(1),nov(2)
> write(69,*)
> endif ! nodezero
> c
> 2000 format(/,2x,'No CI vector file is created')
> 2010 format(/,2x,'CI vectors are stored in ',a32)
> c
> c ------------
> c Tamm-Dancoff
> c ------------
> c
> c Modified for RPA with B = 0
> c
> if (tda) then
> c
> c Write out solution vectors: X (Y=0 in TDA)
> c
> if (nodezero.and.lcivecs) then
> do n=1,nroots
> write(69,*)apbval(n) ! energy of the root
> write(69,*)s2_save(n) ! <S2> value of the root
> do i=1,ipol
> do m=1,nov(i)
> call ga_get(g_x(i),m,m,n,n,r,1)
> write(69,*) r
> enddo ! nov
> enddo ! ipol
> enddo ! nroots
> endif ! nodezero and lcivecs
> c
> c --------------------
> c Full linear response
> c --------------------
> c
> else ! full tddft
> c
> c g_x = X+Y and g_y = X-Y
> c
> do i=1,ipol
> call ga_add(1.0d0,g_x(i), 1.0d0,g_y(i),g_x(i)) ! X+Y
> call ga_add(1.0d0,g_x(i),-2.0d0,g_y(i),g_y(i)) ! X+Y-2Y = X-Y
> enddo
> c
> c Write out vectors: X+Y and X-Y
> c
> if (nodezero.and.lcivecs) then
> do n=1,nroots
> write(69,*)apbval(n) ! energy of the root
> write(69,*)s2_save(n) ! <S2> value of the root
> do i=1,ipol
> do m=1,nov(i)
> call ga_get(g_x(i),m,m,n,n,r,1) ! X vectors
> write(69,*) r
> enddo ! nov
> enddo ! ipol
> c
> do i=1,ipol
> do m=1,nov(i)
> call ga_get(g_y(i),m,m,n,n,r,1) ! Y vectors
> write(69,*) r
> enddo ! nov
> enddo ! ipol
> enddo ! nroots
> endif ! nodezero or lcivecs
> endif ! tda
> c
> if (nodezero.and.lcivecs) close(unit=69)
diff -r nwchem-6.3-src.2013-05-28/src/nwdft/lr_tddft/tddft_davidson.F nwchem-6.3.revision2-src.2013-10-17/src/nwdft/lr_tddft/tddft_davidson.F
8c8
< c $Id: tddft_davidson.F 24076 2013-04-15 16:00:42Z niri $
---
> c $Id: tddft_davidson.F 24309 2013-06-06 18:30:18Z niri $
178d177
< integer vshift
254,259d252
< c Get reference virtual state
< c --------------------------------------------
< if (.not.rtdb_get(rtdb,'tddft:vshift',mt_int,1,vshift))
< & vshift = 0
< c
< c --------------------------------------------
481c474
< 2 lowin,owstart,owend,lewin,ewinl,ewinh,vshift)
---
> 2 lowin,owstart,owend,lewin,ewinl,ewinh)
485c478
< 2 lowin,owstart,owend,lewin,ewinl,ewinh,vshift)
---
> 2 lowin,owstart,owend,lewin,ewinl,ewinh)
500c493
< 2 lowin,owstart,owend,lewin,ewinl,ewinh,vshift)
---
> 2 lowin,owstart,owend,lewin,ewinl,ewinh)
520c513
< 2 lowin,owstart,owend,lewin,ewinl,ewinh,vshift)
---
> 2 lowin,owstart,owend,lewin,ewinl,ewinh)
664c657
< 2 lowin,owstart,owend,lewin,ewinl,ewinh,vshift)
---
> 2 lowin,owstart,owend,lewin,ewinl,ewinh)
668c661
< 2 lowin,owstart,owend,lewin,ewinl,ewinh,vshift)
---
> 2 lowin,owstart,owend,lewin,ewinl,ewinh)
683c676
< 2 lowin,owstart,owend,lewin,ewinl,ewinh,vshift)
---
> 2 lowin,owstart,owend,lewin,ewinl,ewinh)
703c696
< 2 lowin,owstart,owend,lewin,ewinl,ewinh,vshift)
---
> 2 lowin,owstart,owend,lewin,ewinl,ewinh)
801c794
< 7 diff_max,lowin,owstart,owend,lewin,ewinl,ewinh,vshift)
---
> 7 diff_max,lowin,owstart,owend,lewin,ewinl,ewinh)
diff -r nwchem-6.3-src.2013-05-28/src/nwdft/lr_tddft/tddft_init.F nwchem-6.3.revision2-src.2013-10-17/src/nwdft/lr_tddft/tddft_init.F
10c10
< c $Id: tddft_init.F 22895 2012-09-23 01:19:55Z niri $
---
> c $Id: tddft_init.F 24357 2013-07-01 22:46:52Z edo $
112a113,114
> logical xc_got2nd
> external xc_got2nd
125a128,132
>
> if(.not.xc_got2nd()) call errquit(
> A 'analytic 2nds not ready for these XC functionals',0,
> & CAPMIS_ERR)
>
diff -r nwchem-6.3-src.2013-05-28/src/nwdft/lr_tddft/tddft_residual.F nwchem-6.3.revision2-src.2013-10-17/src/nwdft/lr_tddft/tddft_residual.F
7c7
< 6 diff_max,lowin,owstart,owend,lewin,ewinl,ewinh,vshift)
---
> 6 diff_max,lowin,owstart,owend,lewin,ewinl,ewinh)
9c9
< c $Id: tddft_residual.F 24037 2013-04-11 21:10:58Z bert $
---
> c $Id: tddft_residual.F 24309 2013-06-06 18:30:18Z niri $
88d87
< integer vshift
828,832c827
< if (vshift.gt.0) then
< k=nocc(i)+1+vshift
< else
< k=mod(l-1,nmo(i)-nfv(i)-nocc(i))+nocc(i)+1
< end if
---
> k=mod(l-1,nmo(i)-nfv(i)-nocc(i))+nocc(i)+1
929,933c924
< if (vshift.gt.0) then
< k=nocc(i)+1+vshift
< else
< k=mod(l-1,nmo(i)-nfv(i)-nocc(i))+nocc(i)+1
< end if
---
> k=mod(l-1,nmo(i)-nfv(i)-nocc(i))+nocc(i)+1
diff -r nwchem-6.3-src.2013-05-28/src/nwpw/nwpwlib/Parallel/Parallel-tcgmsg.F nwchem-6.3.revision2-src.2013-10-17/src/nwpw/nwpwlib/Parallel/Parallel-tcgmsg.F
2c2
< * $Id: Parallel-tcgmsg.F 22562 2012-06-05 21:17:04Z bylaska $
---
> * $Id: Parallel-tcgmsg.F 24308 2013-06-06 03:34:42Z jhammond $
894c894
< /* determine psr - should be made w/o using tmp array! */
---
> c /* determine psr - should be made w/o using tmp array! */
1033c1033
< /* determine psr - should be made w/o using tmp array! */
---
> c /* determine psr - should be made w/o using tmp array! */
diff -r nwchem-6.3-src.2013-05-28/src/tce/tce_input.F nwchem-6.3.revision2-src.2013-10-17/src/tce/tce_input.F
6c6
< c $Id: tce_input.F 24178 2013-05-03 22:05:45Z kowalski $
---
> c $Id: tce_input.F 24360 2013-07-02 18:09:01Z jhammond $
14c14
< c [FREEZE [[core] (atomic || <integer nfzc default 0>)] \
---
> c [FREEZE [[core] (atomic || <integer nfzc default 0>)]
16,18c16,18
< c [(LCCD||CCD||CCSD||LCCSD||CCSDT||CCSDTQ|| \
< c CCSD(T)||CCSD[T]||QCISD||CISD||CISDT||CISDTQ|| \
< c MBPT2||MBPT3||MBPT4||MP2||MP3||MP4|| \
---
> c [(LCCD||CCD||CCSD||LCCSD||CCSDT||CCSDTQ||
> c CCSD(T)||CCSD[T]||QCISD||CISD||CISDT||CISDTQ||
> c MBPT2||MBPT3||MBPT4||MP2||MP3||MP4||
diff -r nwchem-6.3-src.2013-05-28/src/tce/tce_mo2e_hybrid_2eorb_split.F nwchem-6.3.revision2-src.2013-10-17/src/tce/tce_mo2e_hybrid_2eorb_split.F
3c3
< C $Id: tce_mo2e_hybrid_2eorb_split.F 19706 2010-10-29 17:52:31Z d3y133 $
---
> C $Id: tce_mo2e_hybrid_2eorb_split.F 24292 2013-06-04 01:26:22Z edo $
780c780
< next = nxtask(-nprocs)
---
> next = nxtask(-nprocs,1)
1070c1070
< next = nxtask(-nprocs)
---
> next = nxtask(-nprocs,1)
1297c1297
< next = nxtask(-nprocs)
---
> next = nxtask(-nprocs,1)
1543c1543
< next = nxtask(-nprocs)
---
> next = nxtask(-nprocs,1)
1734c1734
< next = nxtask(-nprocs)
---
> next = nxtask(-nprocs,1)
diff -r nwchem-6.3-src.2013-05-28/src/tce/tce_mo2e_zones_4a_disk_ga_chop_N5.F nwchem-6.3.revision2-src.2013-10-17/src/tce/tce_mo2e_zones_4a_disk_ga_chop_N5.F
4c4
< C $Id: tce_mo2e_zones_4a_disk_ga_chop_N5.F 19706 2010-10-29 17:52:31Z d3y133 $
---
> C $Id: tce_mo2e_zones_4a_disk_ga_chop_N5.F 24330 2013-06-19 22:02:55Z kowalski $
480,483c480,489
< CALL TCE_SORT_4KG_(dbl_mb(k_integral),dbl_mb(k_aux),
< & int_mb(k_range_alpha+g3b-1),nalength(azone4),
< & nalength(azone1),nalength(azone2),
< &2,1,3,4,1.0d0)
---
> ccx CALL TCE_SORT_4KG_(dbl_mb(k_integral),dbl_mb(k_aux),
> ccx & int_mb(k_range_alpha+g3b-1),nalength(azone4),
> ccx & nalength(azone1),nalength(azone2),
> ccx &2,1,3,4,1.0d0)
> c old transpositions
> call TCE_SORT_4(dbl_mb(k_integral),dbl_mb(k_aux),
> & nalength(azone2),nalength(azone1),nalength(azone4),
> & int_mb(k_range_alpha+g3b-1),
> & 1,2,4,3,1.0d0)
> c
517,520c523,530
< CALL TCE_SORT_4KG_(dbl_mb(k_4a),dbl_mb(k_aux),
< & nalength(azone3),nalength(azone4),
< & nalength(azone1),nalength(azone2),
< &2,1,3,4,1.0d0)
---
> ccx CALL TCE_SORT_4KG_(dbl_mb(k_4a),dbl_mb(k_aux),
> ccx & nalength(azone3),nalength(azone4),
> ccx & nalength(azone1),nalength(azone2),
> ccx &2,1,3,4,1.0d0)
> call TCE_SORT_4(dbl_mb(k_4a),dbl_mb(k_aux),
> & nalength(azone2),nalength(azone1),nalength(azone4),
> & nalength(azone3),
> & 1,2,4,3,1.0d0)
553,556c563,572
< CALL TCE_SORT_4KG_(dbl_mb(k_integral),dbl_mb(k_aux),
< & int_mb(k_range_alpha+g3b-1),nalength(azone3),
< & nalength(azone1),nalength(azone2),
< &2,1,3,4,1.0d0)
---
> ccx CALL TCE_SORT_4KG_(dbl_mb(k_integral),dbl_mb(k_aux),
> ccx & int_mb(k_range_alpha+g3b-1),nalength(azone3),
> ccx & nalength(azone1),nalength(azone2),
> ccx &2,1,3,4,1.0d0)
> c old transposition
> CALL TCE_SORT_4(dbl_mb(k_integral),dbl_mb(k_aux),
> 1 nalength(azone2),nalength(azone1),nalength(azone3),
> 2 int_mb(k_range_alpha+g3b-1),
> 3 1,2,4,3,1.0d0)
> c
616,619c632,641
< CALL TCE_SORT_4KG_(dbl_mb(k_integral),dbl_mb(k_aux),
< & int_mb(k_range_alpha+g3b-1),nalength(azone4),
< & nalength(azone1),nalength(azone2),
< &2,1,3,4,1.0d0)
---
> ccx CALL TCE_SORT_4KG_(dbl_mb(k_integral),dbl_mb(k_aux),
> ccx & int_mb(k_range_alpha+g3b-1),nalength(azone4),
> ccx & nalength(azone1),nalength(azone2),
> ccx &2,1,3,4,1.0d0)
> c old transposition
> CALL TCE_SORT_4(dbl_mb(k_integral),dbl_mb(k_aux),
> & nalength(azone2),nalength(azone1),nalength(azone4),
> & int_mb(k_range_alpha+g3b-1),
> & 1,2,4,3,1.0d0)
> c
813,816c835,844
< CALL TCE_SORT_4KG_(dbl_mb(k_integral),dbl_mb(k_aux),
< &int_mb(k_range_alpha+g4b-1),int_mb(k_range_alpha+g3b-1),
< &nalength(azone1),int_mb(k_range_alpha+g2b-1),
< &1,2,4,3,1.0d0)
---
> ccx CALL TCE_SORT_4KG_(dbl_mb(k_integral),dbl_mb(k_aux),
> ccx &int_mb(k_range_alpha+g4b-1),int_mb(k_range_alpha+g3b-1),
> ccx &nalength(azone1),int_mb(k_range_alpha+g2b-1),
> ccx &1,2,4,3,1.0d0)
> c old transposition
> CALL TCE_SORT_4(dbl_mb(k_integral),dbl_mb(k_aux),
> & int_mb(k_range_alpha+g2b-1),nalength(azone1),
> & int_mb(k_range_alpha+g3b-1),int_mb(k_range_alpha+g4b-1),
> & 2,1,3,4,1.0d0)
> c
853,856c881,889
< CALL TCE_SORT_4KG_(dbl_mb(k_2g2a),dbl_mb(k_aux),
< & int_mb(k_range_alpha+g4b-1),int_mb(k_range_alpha+g3b-1),
< & nalength(azone1),nalength(azone2),
< & 1,2,4,3,1.0d0)
---
> ccx CALL TCE_SORT_4KG_(dbl_mb(k_2g2a),dbl_mb(k_aux),
> ccx & int_mb(k_range_alpha+g4b-1),int_mb(k_range_alpha+g3b-1),
> ccx & nalength(azone1),nalength(azone2),
> ccx & 1,2,4,3,1.0d0)
> c old transposition
> CALL TCE_SORT_4(dbl_mb(k_2g2a),dbl_mb(k_aux),
> & nalength(azone2),nalength(azone1),
> & int_mb(k_range_alpha+g3b-1),int_mb(k_range_alpha+g4b-1),
> & 2,1,3,4,1.0d0)
890,893c923,932
< CALL TCE_SORT_4KG_(dbl_mb(k_integral),dbl_mb(k_aux),
< &int_mb(k_range_alpha+g4b-1),int_mb(k_range_alpha+g3b-1),
< &nalength(azone2),int_mb(k_range_alpha+g2b-1),
< &1,2,4,3,1.0d0)
---
> ccx CALL TCE_SORT_4KG_(dbl_mb(k_integral),dbl_mb(k_aux),
> ccx &int_mb(k_range_alpha+g4b-1),int_mb(k_range_alpha+g3b-1),
> ccx &nalength(azone2),int_mb(k_range_alpha+g2b-1),
> ccx &1,2,4,3,1.0d0)
> c old transposition
> CALL TCE_SORT_4(dbl_mb(k_integral),dbl_mb(k_aux),
> & int_mb(k_range_alpha+g2b-1),nalength(azone2),
> & int_mb(k_range_alpha+g3b-1),int_mb(k_range_alpha+g4b-1),
> & 2,1,3,4,1.0d0)
> c
959,962c998,1007
< CALL TCE_SORT_4KG_(dbl_mb(k_integral),dbl_mb(k_aux),
< &int_mb(k_range_alpha+g4b-1),int_mb(k_range_alpha+g3b-1),
< &nalength(azone1),int_mb(k_range_alpha+g2b-1),
< &1,2,4,3,1.0d0)
---
> ccx CALL TCE_SORT_4KG_(dbl_mb(k_integral),dbl_mb(k_aux),
> ccx &int_mb(k_range_alpha+g4b-1),int_mb(k_range_alpha+g3b-1),
> ccx &nalength(azone1),int_mb(k_range_alpha+g2b-1),
> ccx &1,2,4,3,1.0d0)
> c old transposition
> CALL TCE_SORT_4(dbl_mb(k_integral),dbl_mb(k_aux),
> & int_mb(k_range_alpha+g2b-1),nalength(azone1),
> & int_mb(k_range_alpha+g3b-1),int_mb(k_range_alpha+g4b-1),
> & 2,1,3,4,1.0d0)
> c
diff -r nwchem-6.3-src.2013-05-28/src/tce/tce_mo2e_zones_4a_disk_ga_N5.F nwchem-6.3.revision2-src.2013-10-17/src/tce/tce_mo2e_zones_4a_disk_ga_N5.F
4c4
< C $Id: tce_mo2e_zones_4a_disk_ga_N5.F 19706 2010-10-29 17:52:31Z d3y133 $
---
> C $Id: tce_mo2e_zones_4a_disk_ga_N5.F 24328 2013-06-19 17:52:34Z kowalski $
440,443c440,449
< CALL TCE_SORT_4KG_(dbl_mb(k_integral),dbl_mb(k_aux),
< & int_mb(k_range_alpha+g3b-1),nalength(azone4),
< & nalength(azone1),nalength(azone2),
< &2,1,3,4,1.0d0)
---
> ccx CALL TCE_SORT_4KG_(dbl_mb(k_integral),dbl_mb(k_aux),
> ccx & int_mb(k_range_alpha+g3b-1),nalength(azone4),
> ccx & nalength(azone1),nalength(azone2),
> ccx &2,1,3,4,1.0d0)
> c old transpositions
> call TCE_SORT_4(dbl_mb(k_integral),dbl_mb(k_aux),
> & nalength(azone2),nalength(azone1),nalength(azone4),
> & int_mb(k_range_alpha+g3b-1),
> & 1,2,4,3,1.0d0)
> c
477,480c483,491
< CALL TCE_SORT_4KG_(dbl_mb(k_4a),dbl_mb(k_aux),
< & nalength(azone3),nalength(azone4),
< & nalength(azone1),nalength(azone2),
< &2,1,3,4,1.0d0)
---
> ccx CALL TCE_SORT_4KG_(dbl_mb(k_4a),dbl_mb(k_aux),
> ccx & nalength(azone3),nalength(azone4),
> ccx & nalength(azone1),nalength(azone2),
> ccx &2,1,3,4,1.0d0)
> call TCE_SORT_4(dbl_mb(k_4a),dbl_mb(k_aux),
> & nalength(azone2),nalength(azone1),nalength(azone4),
> & nalength(azone3),
> & 1,2,4,3,1.0d0)
> c
513,516c524,533
< CALL TCE_SORT_4KG_(dbl_mb(k_integral),dbl_mb(k_aux),
< & int_mb(k_range_alpha+g3b-1),nalength(azone3),
< & nalength(azone1),nalength(azone2),
< &2,1,3,4,1.0d0)
---
> ccx CALL TCE_SORT_4KG_(dbl_mb(k_integral),dbl_mb(k_aux),
> ccx & int_mb(k_range_alpha+g3b-1),nalength(azone3),
> ccx & nalength(azone1),nalength(azone2),
> ccx &2,1,3,4,1.0d0)
> c old transposition
> CALL TCE_SORT_4(dbl_mb(k_integral),dbl_mb(k_aux),
> 1 nalength(azone2),nalength(azone1),nalength(azone3),
> 2 int_mb(k_range_alpha+g3b-1),
> 3 1,2,4,3,1.0d0)
> c
576,579c593,602
< CALL TCE_SORT_4KG_(dbl_mb(k_integral),dbl_mb(k_aux),
< & int_mb(k_range_alpha+g3b-1),nalength(azone4),
< & nalength(azone1),nalength(azone2),
< &2,1,3,4,1.0d0)
---
> ccx CALL TCE_SORT_4KG_(dbl_mb(k_integral),dbl_mb(k_aux),
> ccx & int_mb(k_range_alpha+g3b-1),nalength(azone4),
> ccx & nalength(azone1),nalength(azone2),
> ccx &2,1,3,4,1.0d0)
> c old transposition
> CALL TCE_SORT_4(dbl_mb(k_integral),dbl_mb(k_aux),
> & nalength(azone2),nalength(azone1),nalength(azone4),
> & int_mb(k_range_alpha+g3b-1),
> & 1,2,4,3,1.0d0)
> c
775,778c798,807
< CALL TCE_SORT_4KG_(dbl_mb(k_integral),dbl_mb(k_aux),
< &int_mb(k_range_alpha+g4b-1),int_mb(k_range_alpha+g3b-1),
< &nalength(azone1),int_mb(k_range_alpha+g2b-1),
< &1,2,4,3,1.0d0)
---
> ccx CALL TCE_SORT_4KG_(dbl_mb(k_integral),dbl_mb(k_aux),
> ccx &int_mb(k_range_alpha+g4b-1),int_mb(k_range_alpha+g3b-1),
> ccx &nalength(azone1),int_mb(k_range_alpha+g2b-1),
> ccx &1,2,4,3,1.0d0)
> c old transposition
> CALL TCE_SORT_4(dbl_mb(k_integral),dbl_mb(k_aux),
> & int_mb(k_range_alpha+g2b-1),nalength(azone1),
> & int_mb(k_range_alpha+g3b-1),int_mb(k_range_alpha+g4b-1),
> & 2,1,3,4,1.0d0)
> c
815,818c844,852
< CALL TCE_SORT_4KG_(dbl_mb(k_2g2a),dbl_mb(k_aux),
< & int_mb(k_range_alpha+g4b-1),int_mb(k_range_alpha+g3b-1),
< & nalength(azone1),nalength(azone2),
< & 1,2,4,3,1.0d0)
---
> ccx CALL TCE_SORT_4KG_(dbl_mb(k_2g2a),dbl_mb(k_aux),
> ccx & int_mb(k_range_alpha+g4b-1),int_mb(k_range_alpha+g3b-1),
> ccx & nalength(azone1),nalength(azone2),
> ccx & 1,2,4,3,1.0d0)
> c old transposition
> CALL TCE_SORT_4(dbl_mb(k_2g2a),dbl_mb(k_aux),
> & nalength(azone2),nalength(azone1),
> & int_mb(k_range_alpha+g3b-1),int_mb(k_range_alpha+g4b-1),
> & 2,1,3,4,1.0d0)
852,855c886,895
< CALL TCE_SORT_4KG_(dbl_mb(k_integral),dbl_mb(k_aux),
< &int_mb(k_range_alpha+g4b-1),int_mb(k_range_alpha+g3b-1),
< &nalength(azone2),int_mb(k_range_alpha+g2b-1),
< &1,2,4,3,1.0d0)
---
> ccx CALL TCE_SORT_4KG_(dbl_mb(k_integral),dbl_mb(k_aux),
> ccx &int_mb(k_range_alpha+g4b-1),int_mb(k_range_alpha+g3b-1),
> ccx &nalength(azone2),int_mb(k_range_alpha+g2b-1),
> ccx &1,2,4,3,1.0d0)
> c old transposition
> CALL TCE_SORT_4(dbl_mb(k_integral),dbl_mb(k_aux),
> & int_mb(k_range_alpha+g2b-1),nalength(azone2),
> & int_mb(k_range_alpha+g3b-1),int_mb(k_range_alpha+g4b-1),
> & 2,1,3,4,1.0d0)
> c
921,924c961,970
< CALL TCE_SORT_4KG_(dbl_mb(k_integral),dbl_mb(k_aux),
< &int_mb(k_range_alpha+g4b-1),int_mb(k_range_alpha+g3b-1),
< &nalength(azone1),int_mb(k_range_alpha+g2b-1),
< &1,2,4,3,1.0d0)
---
> ccx CALL TCE_SORT_4KG_(dbl_mb(k_integral),dbl_mb(k_aux),
> ccx &int_mb(k_range_alpha+g4b-1),int_mb(k_range_alpha+g3b-1),
> ccx &nalength(azone1),int_mb(k_range_alpha+g2b-1),
> ccx &1,2,4,3,1.0d0)
> c old transposition
> CALL TCE_SORT_4(dbl_mb(k_integral),dbl_mb(k_aux),
> & int_mb(k_range_alpha+g2b-1),nalength(azone1),
> & int_mb(k_range_alpha+g3b-1),int_mb(k_range_alpha+g4b-1),
> & 2,1,3,4,1.0d0)
> c
1011c1057
< c write(6,*)'DONE --- DONE ---- DONE ---- DONE'
---
> c write(6,*)'DONE --- DONE ---- DONE ---- DONE'
diff -r nwchem-6.3-src.2013-05-28/src/tools/GNUmakefile nwchem-6.3.revision2-src.2013-10-17/src/tools/GNUmakefile
335a336,338
> ifdef EXTERNAL_ARMCI_PATH
> MAYBE_ARMCI = --with-armci=$(EXTERNAL_ARMCI_PATH)
> else
336a340
> endif
diff -r nwchem-6.3-src.2013-05-28/src/util/util_nwchem_version.F nwchem-6.3.revision2-src.2013-10-17/src/util/util_nwchem_version.F
4c4
< nwrev="24277"
---
> nwrev="24652"
Only in nwchem-6.3-src.2013-05-28/: svnlog
525. Briefly: rotating molecule during optimisation in Gaussian
Most people who have used gaussian will be familiar with molecules that are rotated multiple times during optimisation. Occasionally, the molecule is rotated repeatedly without any sign of convergence, and without any changes in atom positions.
Uploading the video to blogspot has lead to some distortion (i.e. the molecule is translated -- look at the x,y,z axes in the bottom left) but the general behaviour should still be clear:
The energies aren't really changing:
Solution:
Turning off rotation using 'nosymm' might yield faster convergence:
In ECCE, just uncheck 'Use available symmetry'.
Note that NoSymm doesn't turn off symmetry completely -- it just prevent reorientation:
From http://www.gaussian.com/g_tech/g_ur/k_symmetry.htm
How the figures were made:
First I used this script to extract the .xyz coordinates of the geometry steps:
Then I turned all the .xyz files into one .xyz file:
Which I then opened in vmd with a view to make a video. Select New Molecule and load structure.xyz. Then go to Extensions, Visualization/Movie Maker. Making a movie using VMD didn't yield to anything of sufficient quality. Instead, I selected Tachyon as the renderer. Under Movie Settings I unchecked Delete Image Files.
Once I had the ppm files I did
The key to getting a decent quality video was picking a high enough bit rate, which is probably obvious to most people who know what bit rate means, but not to a happy amateur like myself (well, now it is).
I made the energy plot using gnuplot and the energies.dat file which the python script above generates.
Uploading the video to blogspot has lead to some distortion (i.e. the molecule is translated -- look at the x,y,z axes in the bottom left) but the general behaviour should still be clear:
The energies aren't really changing:
Solution:
Turning off rotation using 'nosymm' might yield faster convergence:
#P rB3LYP/GEN 5D Opt=() Freq=() SCF=(MaxCycle=128 ) NoSymm Punch=(MO)
In ECCE, just uncheck 'Use available symmetry'.
Note that NoSymm doesn't turn off symmetry completely -- it just prevent reorientation:
From http://www.gaussian.com/g_tech/g_ur/k_symmetry.htm
The NoSymmetry keyword prevents molecule reorientation and causes all computations to be performed in the input orientation (although the program still attempts to identify the appropriate point group). Symmetry use can be completely disabled by Symmetry=None; use this option if NoSymm generates an error when identifying the point group.
How the figures were made:
First I used this script to extract the .xyz coordinates of the geometry steps:
#!/usr/bin/python
import sys
def getrawdata(infile):
f=open(infile,'r')
opt=0
geo=0
struct=[]
structure=[]
energies=[]
energy=[]
for line in f:
if opt==1 and geo==1 and not ("---" in line):
structure+=[line.rstrip()]
if 'Coordinates (Angstroms)' in line:
if opt==0:
opt=1
structure=[]
if opt==1 and "--------------------------" in line:
if geo==0:
geo=1
elif geo==1:
geo=0
opt=0
if 'SCF Done' in line:
energy=filter(None,line.rstrip('\n').split(' '))
# if 'Optimization completed' in line and (opt==0 and geo==0):
energies+=[float(energy[4])]
opt=0
geo=0
struct+=[structure]
structure=[]
return struct, energies
def periodictable(elementnumber):
ptable={1:'H',2:'He',\
3:'Li', 4:'Be',5:'B',6:'C',7:'N',8:'O',9:'F',10:'Ne',\
11:'Na',12:'Mg',13:'Al',14:'Si',15:'P',16:'S',17:'Cl',18:'Ar',\
19:'K',20:'Ca',\
21:'Sc',22:'Ti',23:'V',24:'Cr',25:'Mn',26:'Fe',27:'Co',28:'Ni',29:'Cu',30:'Zn',\
31:'Ga',32:'Ge',33:'As',34:'Se',35:'Br',36:'Kr',\
37:'Rb',38:'Sr',\
39:'Y',40:'Zr',41:'Nb',42:'Mo',43:'Tc',44:'Ru',45:'Rh',46:'Pd',47:'Ag',48:'Cd',\
49:'In',50:'Sn',51:'Sb',52:'Te',53:'I',54:'Xe',\
55:'Cs',56:'Ba',\
57:'La',58:'Ce',59:'Pr',60:'Nd',61:'Pm',62:'Sm',63:'Eu',64:'Gd',65:'Tb',66:'Dy',67:'Ho',68:'Er',69:'Tm',70:'Yb',71:'Lu',\
72:'Hf', 73:'Ta', 74:'W',75:'Re', 76:'Os', 77:'Ir',78:'Pt', 79:'Au', 80:'Hg',\
81:'Tl', 82:'Pb', 83:'Bi',84:'Po',85:'At',86:'Rn',\
87:'Fr',88:'Ra',\
89:'Ac',90:'Th',91:'Pa',92:'U',93:'Np',94:'Pu',95:'Am',96:'Cm',97:'Bk',98:'Cf',99:'Es',100:'Fm',101:'Md',102:'No',\
103:'Lr',104:'Rf',105:'Db',106:'Sg',107:'Bh',108:'Hs',109:'Mt',110:'Ds',111:'Rg',112:'Cn',\
113:'Uut',114:'Fl',115:'Uup',116:'Lv',117:'Uus',118:'Uuo'}
element=ptable[elementnumber]
return element
def genxyzstring(coords,elementnumber):
x_str='%10.5f'% coords[0]
y_str='%10.5f'% coords[1]
z_str='%10.5f'% coords[2]
element=periodictable(int(elementnumber))
xyz_string=element+(3-len(element))*' '+10*' '+\
(8-len(x_str))*' '+x_str+10*' '+(8-len(y_str))*' '+y_str+10*' '+(8-len(z_str))*' '+z_str+'\n'
return xyz_string
def getstructures(rawdata):
n=0
for structure in rawdata:
n=n+1
num="%03d" % (n,)
g=open('structure_'+num+'.xyz','w')
itson=False
cartesian=[]
for item in structure:
coords=filter(None,item.split(' '))
coordinates=[float(coords[3]),float(coords[4]),float(coords[5])]
element=coords[1]
cartesian+=[genxyzstring(coordinates,element)]
g.write(str(len(cartesian))+'\n')
g.write('Structure '+str(n)+'\n')
for line in cartesian:
g.write(line)
g.close()
cartesian=[]
return 0
if __name__ == "__main__":
infile=sys.argv[1]
rawdata,energies=getrawdata(infile)
structures=getstructures(rawdata)
g=open('energies.dat','w')
for n in range(0,len(energies)):
g.write(str(n)+'\t'+str(energies[n])+'\n')
g.close()
Then I turned all the .xyz files into one .xyz file:
cat *.xyz > structures.xyz
Which I then opened in vmd with a view to make a video. Select New Molecule and load structure.xyz. Then go to Extensions, Visualization/Movie Maker. Making a movie using VMD didn't yield to anything of sufficient quality. Instead, I selected Tachyon as the renderer. Under Movie Settings I unchecked Delete Image Files.
Once I had the ppm files I did
ffmpeg -r 2 -i symm.%05d.ppm -vcodec mpeg4 -b 5000k video.avi
The key to getting a decent quality video was picking a high enough bit rate, which is probably obvious to most people who know what bit rate means, but not to a happy amateur like myself (well, now it is).
I made the energy plot using gnuplot and the energies.dat file which the python script above generates.