From amar.b.007 at gmail.com Sun Jun 10 14:55:44 2012 From: amar.b.007 at gmail.com (Dr. Amar Bahadur) Date: Sun, 10 Jun 2012 18:25:44 +0530 Subject: [xcrysden] Reg: Xcrysden download Message-ID: Dear Sir, I have to installed Xcrysden on UBUNTU 12.04. Please help me to suggest which one of these I download and install 1. xc-1.4.1bin-linuxPC-static.tar.gz 2. xc-1.4.1bin-linuxPC-shared.tar.gz 3. xcrysden-1.5.53.tar.gz -- Kind Regards. ================== Amar Bahadur (Department of Physics) Kamla Nehru Institute of Physical and Social Sciences, Sultanpur- 228 118 (U.P.) India Email: amar.b.007 at gmail.com Mob.-+91-9451431428, 9044160486 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20120610/7f190345/attachment.htm From amar.b.007 at gmail.com Sun Jun 10 15:05:12 2012 From: amar.b.007 at gmail.com (Dr. Amar Bahadur) Date: Sun, 10 Jun 2012 18:35:12 +0530 Subject: [xcrysden] Fwd: Reg: Xcrysden download In-Reply-To: References: Message-ID: Dear Sir, I have to installed Xcrysden on UBUNTU 12.04. Please help me to suggest which one of these I download and install 1. *Source package:* xcrysden-1.5.53.tar.gz 2. *Linux x86_64 binary packages:* Shared: xcrysden-1.5.53-linux_x86_64-shared.tar.gz Semishared: xcrysden-1.5.53-linux_x86_64-semishared.tar.gz -- Kind Regards. ================== Amar Bahadur (Department of Physics) Kamla Nehru Institute of Physical and Social Sciences, Sultanpur- 228 118 (U.P.) India Email: amar.b.007 at gmail.com Mob.-+91-9451431428, 9044160486 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20120610/bb3f86aa/attachment.htm From amar.b.007 at gmail.com Sun Jun 10 17:33:13 2012 From: amar.b.007 at gmail.com (Dr. Amar Bahadur) Date: Sun, 10 Jun 2012 21:03:13 +0530 Subject: [xcrysden] (no subject) Message-ID: -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20120610/618cb4cc/attachment.htm From mohnish.iitk at gmail.com Wed Jun 13 13:30:03 2012 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Wed, 13 Jun 2012 17:00:03 +0530 Subject: [xcrysden] Fwd: Reg: Xcrysden download In-Reply-To: References: Message-ID: Semishared: xcrysden-1.5.53-linux_x86_64-semishared.tar.gz On Sun, Jun 10, 2012 at 6:35 PM, Dr. Amar Bahadur wrote: > Dear Sir, > I have to installed Xcrysden on UBUNTU 12.04. Please help > me to suggest which one of these I download and install > 1. *Source package:* xcrysden-1.5.53.tar.gz > 2. *Linux x86_64 binary packages:* > Shared: xcrysden-1.5.53-linux_x86_64-shared.tar.gz > Semishared: xcrysden-1.5.53-linux_x86_64-semishared.tar.gz > > -- > Kind Regards. > > ================== > Amar Bahadur > (Department of Physics) > Kamla Nehru Institute of Physical and Social Sciences, > Sultanpur- 228 118 (U.P.) India > Email: amar.b.007 at gmail.com > Mob.-+91-9451431428, 9044160486 > > > > > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > > -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey BTech-Mtech, IIT Kanpur Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20120613/da6135e1/attachment.htm From i_camps at yahoo.com.br Wed Jun 13 23:29:29 2012 From: i_camps at yahoo.com.br (I. Camps) Date: Wed, 13 Jun 2012 18:29:29 -0300 Subject: [xcrysden] << Installing XCrysDen in CentOS 5.8 64bits >> Message-ID: Dear XCrysDen users, I am trying to install XCrysDen in CentOS 5.8 64bits unsuccessfully. I downloaded all the 1.5 shared and semishared versions. Also, I tried to compiled from source. In all cases, there is always a library that is not in my system and whenever I look for it, it is not available to my system version. Did anyone had installed XCrysDen in CentOS 5.8 64bits successfully? Bellow is the information about my system. I had CentOS 6.0 64bits, where XCrysDen ran ok, but after a system actualization, my laptop did not boot anymore, so I got back to version 5.x. Best regards, and thanks in advance, Camps ***************************** Information for general problems. [code] == BEGIN uname -rmi == 2.6.18-308.8.1.el5.centos.plus x86_64 x86_64 == END uname -rmi == == BEGIN rpm -qa \*-release\* == centos-release-notes-5.8-0 centos-release-5-8.el5.centos rpmforge-release-0.5.2-2.el5. rf adobe-release-i386-1.0-1 epel-release-5-4 == END rpm -qa \*-release\* == == BEGIN cat /etc/redhat-release == CentOS release 5.8 (Final) == END cat /etc/redhat-release == == BEGIN getenforce == Disabled == END getenforce == == BEGIN free -m == total used free shared buffers cached Mem: 7923 738 7184 0 32 421 -/+ buffers/cache: 284 7639 Swap: 0 0 0 == END free -m == == BEGIN rpm -qa yum\* rpm-\* python | sort == python-2.4.3-46.el5 rpm-build-4.4.2.3-28.el5_8 rpm-devel-4.4.2.3-28.el5_8 rpm-devel-4.4.2.3-28.el5_8 rpm-libs-4.4.2.3-28.el5_8 rpm-libs-4.4.2.3-28.el5_8 rpm-python-4.4.2.3-28.el5_8 yum-3.2.22-39.el5.centos yum-fastestmirror-1.1.16-21.el5.centos yum-metadata-parser-1.1.2-3.el5.centos yum-priorities-1.1.16-21.el5.centos yum-updatesd-0.9-2.el5 == END rpm -qa yum\* rpm-\* python | sort == == BEGIN ls /etc/yum.repos.d == adobe-linux-i386.repo CentOS-Base.repo CentOS-Base.repo~ CentOS-Debuginfo.repo CentOS-Media.repo CentOS-Vault.repo epel.repo epel.repo~ epel-testing.repo mirrors-rpmforge mirrors-rpmforge-extras mirrors-rpmforge-testing rpmforge.repo rpmforge.repo~ == END ls /etc/yum.repos.d == == BEGIN cat /etc/yum.conf == [main] cachedir=/var/cache/yum keepcache=0 debuglevel=2 logfile=/var/log/yum.log distroverpkg=redhat-release tolerant=1 exactarch=1 obsoletes=1 gpgcheck=1 plugins=1 bugtracker_url=http://bugs.centos.org/yum5bug # Note: yum-RHN-plugin doesn't honor this. metadata_expire=1h installonly_limit = 5 # PUT YOUR REPOS HERE OR IN separate files named file.repo # in /etc/yum.repos.d == END cat /etc/yum.conf == == BEGIN yum repolist all == Loaded plugins: fastestmirror, priorities Loading mirror speeds from cached hostfile * base: mirror.ueg.br * centosplus: centos.redeminastelecom.com.br * epel: mirror.metrocast.net * extras: mirror.ueg.br * rpmforge: mirror.us.leaseweb.net * rpmforge-extras: mirror.us.leaseweb.net * updates: mirror.ueg.br 610 packages excluded due to repository priority protections repo id repo name status C5.0-base CentOS-5.0 - Base disabled C5.0-centosplus CentOS-5.0 - Plus disabled C5.0-extras CentOS-5.0 - Extras disabled C5.0-updates CentOS-5.0 - Updates disabled C5.1-base CentOS-5.1 - Base disabled C5.1-centosplus CentOS-5.1 - Plus disabled C5.1-extras CentOS-5.1 - Extras disabled C5.1-updates CentOS-5.1 - Updates disabled C5.2-base CentOS-5.2 - Base disabled C5.2-centosplus CentOS-5.2 - Plus disabled C5.2-extras CentOS-5.2 - Extras disabled C5.2-updates CentOS-5.2 - Updates disabled C5.3-base CentOS-5.3 - Base disabled C5.3-centosplus CentOS-5.3 - Plus disabled C5.3-extras CentOS-5.3 - Extras disabled C5.3-updates CentOS-5.3 - Updates disabled C5.4-base CentOS-5.4 - Base disabled C5.4-centosplus CentOS-5.4 - Plus disabled C5.4-extras CentOS-5.4 - Extras disabled C5.4-updates CentOS-5.4 - Updates disabled C5.5-base CentOS-5.5 - Base disabled C5.5-centosplus CentOS-5.5 - Plus disabled C5.5-extras CentOS-5.5 - Extras disabled C5.5-updates CentOS-5.5 - Updates disabled C5.6-base CentOS-5.6 - Base disabled C5.6-centosplus CentOS-5.6 - Plus disabled C5.6-extras CentOS-5.6 - Extras disabled C5.6-updates CentOS-5.6 - Updates disabled C5.7-base CentOS-5.7 - Base disabled C5.7-centosplus CentOS-5.7 - Plus disabled C5.7-extras CentOS-5.7 - Extras disabled C5.7-updates CentOS-5.7 - Updates disabled adobe-linux-i386 Adobe Systems Incorporated enabled: 16+1 base CentOS-5 - Base enabled: 3,591 c5-media CentOS-5 - Media disabled centosplus CentOS-5 - Plus enabled: 50 contrib CentOS-5 - Contrib disabled debug CentOS-5 - Debuginfo disabled epel Extra Packages for Enterprise Linux 5 enabled: 6,754+288 epel-debuginfo Extra Packages for Enterprise Linux 5 disabled epel-source Extra Packages for Enterprise Linux 5 disabled epel-testing Extra Packages for Enterprise Linux 5 disabled epel-testing-debuginfo Extra Packages for Enterprise Linux 5 disabled epel-testing-source Extra Packages for Enterprise Linux 5 disabled extras CentOS-5 - Extras enabled: 273 rpmforge RHEL 5 - RPMforge.net - dag enabled: 10,930+131 rpmforge-extras RHEL 5 - RPMforge.net - extras enabled: 42+185 rpmforge-testing RHEL 5 - RPMforge.net - testing disabled updates CentOS-5 - Updates enabled: 609 repolist: 22,265 == END yum repolist all == == BEGIN egrep 'include|exclude' /etc/yum.repos.d/*.repo == == END egrep 'include|exclude' /etc/yum.repos.d/*.repo == == BEGIN sed -n -e "/^\[/h; /priority *=/{ G; s/\n/ /; s/ity=/ity = /; p }" /etc/yum.repos.d/*.repo | sort -k3n == priority = 1 [base] priority = 1 [centosplus] priority = 1 [extras] priority = 1 [updates] priority = 30 [epel] priority = 30 [epel-debuginfo] priority = 30 [epel-source] priority = 30 [rpmforge] priority = 30 [rpmforge-extras] == END sed -n -e "/^\[/h; /priority *=/{ G; s/\n/ /; s/ity=/ity = /; p }" /etc/yum.repos.d/*.repo | sort -k3n == == BEGIN cat /etc/fstab == LABEL=/ / ext3 defaults 1 1 tmpfs /dev/shm tmpfs defaults 0 0 devpts /dev/pts devpts gid=5,mode=620 0 0 sysfs /sys sysfs defaults 0 0 proc /proc proc defaults 0 0 /dev/sda2 /mnt/Win7 ntfs-3g rw,umask=0000,defaults 0 0 /dev/sda3 /mnt/Dados ntfs-3g rw,umask=0000,defaults 0 0 == END cat /etc/fstab == == BEGIN df -h == Filesystem Size Used Avail Use% Mounted on /dev/sda5 40G 14G 24G 38% / tmpfs 3.9G 0 3.9G 0% /dev/shm /dev/sda2 176G 154G 22G 88% /mnt/Win7 /dev/sda3 380G 285G 96G 75% /mnt/Dados == END df -h == == BEGIN fdisk -l == Disk /dev/sda: 640.1 GB, 640135028736 bytes 255 heads, 63 sectors/track, 77825 cylinders Units = cylinders of 16065 * 512 = 8225280 bytes Device Boot Start End Blocks Id System /dev/sda1 * 1 13 102400 7 HPFS/NTFS Partition 1 does not end on cylinder boundary. /dev/sda2 13 22960 184320000 7 HPFS/NTFS /dev/sda3 22960 72561 398417920 7 HPFS/NTFS Partition 3 does not end on cylinder boundary. /dev/sda4 72562 77825 42283080 5 Extended /dev/sda5 72562 77825 42283048+ 83 Linux == END fdisk -l == == BEGIN blkid == /dev/sda5: LABEL="/" UUID="5a6f4486-10d5-4c74-99f5-371935a24ae2" TYPE="ext3" /dev/sda1: TYPE="ntfs" /dev/sda2: TYPE="ntfs" /dev/sda3: TYPE="ntfs" == END blkid == == BEGIN cat /proc/mdstat == Personalities : unused devices: == END cat /proc/mdstat == == BEGIN pvs == == END pvs == == BEGIN vgs == No volume groups found == END vgs == == BEGIN lvs == No volume groups found == END lvs == == BEGIN rpm -qa kernel\* | sort == kernel-2.6.18-194.el5 kernel-2.6.18-308.8.1.el5 kernel-2.6.18-308.8.1.el5.centos.plus kernel-devel-2.6.18-194.el5 kernel-devel-2.6.18-308.8.1.el5 kernel-devel-2.6.18-308.8.1.el5.centos.plus kernel-headers-2.6.18-308.8.1.el5.centos.plus == END rpm -qa kernel\* | sort == == BEGIN lspci -nn == 00:00.0 Host bridge [0600]: Intel Corporation Core Processor DMI [8086:d132] (rev 11) 00:03.0 PCI bridge [0604]: Intel Corporation Core Processor PCI Express Root Port 1 [8086:d138] (rev 11) 00:08.0 System peripheral [0880]: Intel Corporation Core Processor System Management Registers [8086:d155] (rev 11) 00:08.1 System peripheral [0880]: Intel Corporation Core Processor Semaphore and Scratchpad Registers [8086:d156] (rev 11) 00:08.2 System peripheral [0880]: Intel Corporation Core Processor System Control and Status Registers [8086:d157] (rev 11) 00:08.3 System peripheral [0880]: Intel Corporation Core Processor Miscellaneous Registers [8086:d158] (rev 11) 00:10.0 System peripheral [0880]: Intel Corporation Core Processor QPI Link [8086:d150] (rev 11) 00:10.1 System peripheral [0880]: Intel Corporation Core Processor QPI Routing and Protocol Registers [8086:d151] (rev 11) 00:16.0 Communication controller [0780]: Intel Corporation 5 Series/3400 Series Chipset HECI Controller [8086:3b64] (rev 06) 00:1a.0 USB controller [0c03]: Intel Corporation 5 Series/3400 Series Chipset USB2 Enhanced Host Controller [8086:3b3c] (rev 06) 00:1b.0 Audio device [0403]: Intel Corporation 5 Series/3400 Series Chipset High Definition Audio [8086:3b56] (rev 06) 00:1c.0 PCI bridge [0604]: Intel Corporation 5 Series/3400 Series Chipset PCI Express Root Port 1 [8086:3b42] (rev 06) 00:1c.1 PCI bridge [0604]: Intel Corporation 5 Series/3400 Series Chipset PCI Express Root Port 2 [8086:3b44] (rev 06) 00:1c.2 PCI bridge [0604]: Intel Corporation 5 Series/3400 Series Chipset PCI Express Root Port 3 [8086:3b46] (rev 06) 00:1c.4 PCI bridge [0604]: Intel Corporation 5 Series/3400 Series Chipset PCI Express Root Port 5 [8086:3b4a] (rev 06) 00:1c.5 PCI bridge [0604]: Intel Corporation 5 Series/3400 Series Chipset PCI Express Root Port 6 [8086:3b4c] (rev 06) 00:1d.0 USB controller [0c03]: Intel Corporation 5 Series/3400 Series Chipset USB2 Enhanced Host Controller [8086:3b34] (rev 06) 00:1e.0 PCI bridge [0604]: Intel Corporation 82801 Mobile PCI Bridge [8086:2448] (rev a6) 00:1f.0 ISA bridge [0601]: Intel Corporation Mobile 5 Series Chipset LPC Interface Controller [8086:3b09] (rev 06) 00:1f.2 SATA controller [0106]: Intel Corporation 5 Series/3400 Series Chipset 4 port SATA AHCI Controller [8086:3b29] (rev 06) 00:1f.3 SMBus [0c05]: Intel Corporation 5 Series/3400 Series Chipset SMBus Controller [8086:3b30] (rev 06) 01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GT215 [GeForce GTS 360M] [10de:0cb1] (rev a2) 01:00.1 Audio device [0403]: NVIDIA Corporation High Definition Audio Controller [10de:0be4] (rev a1) 03:00.0 Network controller [0280]: Atheros Communications Inc. AR9285 Wireless Network Adapter (PCI-Express) [168c:002b] (rev 01) 06:00.0 SD Host controller [0805]: Ricoh Co Ltd MMC/SD Host Controller [1180:e822] (rev 01) 06:00.1 System peripheral [0880]: Ricoh Co Ltd Memory Stick Host Controller [1180:e230] (rev 01) 06:00.2 System peripheral [0880]: Ricoh Co Ltd Device [1180:e852] (rev 01) 06:00.3 FireWire (IEEE 1394) [0c00]: Ricoh Co Ltd FireWire Host Controller [1180:e832] (rev 01) 07:00.0 Ethernet controller [0200]: Atheros Communications Inc. AR8131 Gigabit Ethernet [1969:1063] (rev c0) 3f:00.0 Host bridge [0600]: Intel Corporation Core Processor QuickPath Architecture Generic Non-Core Registers [8086:2c52] (rev 04) 3f:00.1 Host bridge [0600]: Intel Corporation Core Processor QuickPath Architecture System Address Decoder [8086:2c81] (rev 04) 3f:02.0 Host bridge [0600]: Intel Corporation Core Processor QPI Link 0 [8086:2c90] (rev 04) 3f:02.1 Host bridge [0600]: Intel Corporation Core Processor QPI Physical 0 [8086:2c91] (rev 04) 3f:03.0 Host bridge [0600]: Intel Corporation Core Processor Integrated Memory Controller [8086:2c98] (rev 04) 3f:03.1 Host bridge [0600]: Intel Corporation Core Processor Integrated Memory Controller Target Address Decoder [8086:2c99] (rev 04) 3f:03.4 Host bridge [0600]: Intel Corporation Core Processor Integrated Memory Controller Test Registers [8086:2c9c] (rev 04) 3f:04.0 Host bridge [0600]: Intel Corporation Core Processor Integrated Memory Controller Channel 0 Control Registers [8086:2ca0] (rev 04) 3f:04.1 Host bridge [0600]: Intel Corporation Core Processor Integrated Memory Controller Channel 0 Address Registers [8086:2ca1] (rev 04) 3f:04.2 Host bridge [0600]: Intel Corporation Core Processor Integrated Memory Controller Channel 0 Rank Registers [8086:2ca2] (rev 04) 3f:04.3 Host bridge [0600]: Intel Corporation Core Processor Integrated Memory Controller Channel 0 Thermal Control Registers [8086:2ca3] (rev 04) 3f:05.0 Host bridge [0600]: Intel Corporation Core Processor Integrated Memory Controller Channel 1 Control Registers [8086:2ca8] (rev 04) 3f:05.1 Host bridge [0600]: Intel Corporation Core Processor Integrated Memory Controller Channel 1 Address Registers [8086:2ca9] (rev 04) 3f:05.2 Host bridge [0600]: Intel Corporation Core Processor Integrated Memory Controller Channel 1 Rank Registers [8086:2caa] (rev 04) 3f:05.3 Host bridge [0600]: Intel Corporation Core Processor Integrated Memory Controller Channel 1 Thermal Control Registers [8086:2cab] (rev 04) == END lspci -nn == == BEGIN lsusb == Protocol spec without prior Class and Subclass spec at line 4297 Bus 002 Device 003: ID 045e:00e1 Microsoft Corp. Wireless Laser Mouse 6000 Reciever Bus 002 Device 001: ID 0000:0000 Bus 002 Device 002: ID 8087:0020 Intel Corp. Integrated Rate Matching Hub Bus 001 Device 001: ID 0000:0000 Bus 001 Device 002: ID 8087:0020 Intel Corp. Integrated Rate Matching Hub Bus 001 Device 003: ID 0b05:1751 ASUSTek Computer, Inc. BT-253 Bluetooth Adapter Bus 001 Device 004: ID 04f2:b106 Chicony Electronics Co., Ltd == END lsusb == == BEGIN rpm -qa kmod\* kmdl\* == == END rpm -qa kmod\* kmdl\* == [/code] -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20120613/758a4647/attachment-0001.htm From zchen at blem.ac.cn Thu Jun 14 10:57:20 2012 From: zchen at blem.ac.cn (ZhenChen) Date: Thu, 14 Jun 2012 16:57:20 +0800 Subject: [xcrysden] how to render pre-calculted 3D electron density for Wien2K in Xcrysden? Message-ID: <201206141657205155941@blem.ac.cn> Dear xcrysden users, I have a question about wien2k electron density plot. As I know, we can use xcrysden to plot precalculated 2D electron density and to render and calculate 3D electron density using 'x -lapw5' command simutaneously. I am eager to know if it is convenient to render pre-calculated 3D electron density? In my case, I use Wien2k to calculate electron density in a supercomputer center and plot it in my personal computer, so I can't calculate electron density in my computer where the xcrysden runs. So my question is: is it easy to just take off the wien2k command during a 3D electron density calculation and use pre-calculated data to render 3D electron density, which is similar as plotting pre-calculated 2D electron density. What should I modify about the commands? Do I have to write a whole new script? What files do I have to get before a plot? Any response and suggestions will be highly appreciated! Best regards! 2012-06-14 ?? PhD. candidate Zhen Chen ------------------------------ Prof. Jianqi Li's group, A06 Beijing Laboratory of Electron Microscopy Institute of Physics Chinese Academy of Sciences P. O. Box 603 Beijing 100190, China Tel: 86-10-82648001 URL: http://www.blem.ac.cn/english/study-A06-1.asp ????????zchen at blem.ac.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20120614/1edeb60a/attachment.htm From natalie at wfu.edu Sat Jun 16 00:29:07 2012 From: natalie at wfu.edu (Holzwarth, Natalie) Date: Fri, 15 Jun 2012 18:29:07 -0400 Subject: [xcrysden] Difficulty compiling Xcrysden 1.5.53 Message-ID: Dear Xcrysden developers, In compiling the 1.5.53 version of Xcrysden I ran into the following error which was generated in ubuntu 10.4 and 12.04 using the gcc compiler. I briefly scanned the archive and could not find previous instances of this problem. gcc -g -static -ansi -ffast-math -funroll-loops -DUSE_FONTS -pedantic -Wall -DUSE_FONTS -I/home/natalie/Sharedata/Visualization/Xcrysden/xcrysden-1.5.53/external/src/tcl8.5.11/generic -I/home/natalie/Sharedata/Visualization/Xcrysden/xcrysden-1.5.53/external/src/tk8.5.11/generic -I/home/natalie/Sharedata/Visualization/Xcrysden/xcrysden-1.5.53/external/include -c gl2ps.c gl2ps.c: In function ?gl2psPutPDFText?: gl2ps.c:3416: error: ?M_PI? undeclared (first use in this function) gl2ps.c:3416: error: (Each undeclared identifier is reported only once gl2ps.c:3416: error: for each function it appears in.) I notice the M_Pi is defined in the subroutine shank_Hinv.c, but it apparently does not know the value in gl2ps.c. Thanks in advance for any suggestions on how to fix this problem. Sincerely, Natalie Holzwarth N. A. W. Holzwarth email: natalie at wfu.edu Department of Physics web: http://www.wfu.edu/~natalie Wake Forest University phone: 1-336-758-5510 Winston-Salem, NC 27109 USA office: Rm. 300 Olin Physical Lab -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20120615/8f18b6ab/attachment.htm From natalie at wfu.edu Mon Jun 18 23:20:32 2012 From: natalie at wfu.edu (Holzwarth, Natalie) Date: Mon, 18 Jun 2012 17:20:32 -0400 Subject: [xcrysden] Difficulty compiling Xcrysden 1.5.53 In-Reply-To: References: Message-ID: Dear Xcrysden developers, I was able to figure out a workable solution. Apparently it had something to do with Make.sys-static not working well. For some reason Make.sys-share works well and knows what M_Pi is. Thanks for your beautiful software package. We have been relying on it for many visualizations. Natalie N. A. W. Holzwarth email: natalie at wfu.edu Department of Physics web: http://www.wfu.edu/~natalie Wake Forest University phone: 1-336-758-5510 Winston-Salem, NC 27109 USA office: Rm. 300 Olin Physical Lab On Fri, Jun 15, 2012 at 6:29 PM, Holzwarth, Natalie wrote: > Dear Xcrysden developers, > In compiling the 1.5.53 version of Xcrysden I ran into the > following error which was generated in ubuntu 10.4 and 12.04 using the gcc > compiler. I briefly scanned the archive and could not find previous > instances of this problem. > > gcc -g -static -ansi -ffast-math -funroll-loops -DUSE_FONTS -pedantic > -Wall -DUSE_FONTS > -I/home/natalie/Sharedata/Visualization/Xcrysden/xcrysden-1.5.53/external/src/tcl8.5.11/generic > -I/home/natalie/Sharedata/Visualization/Xcrysden/xcrysden-1.5.53/external/src/tk8.5.11/generic > -I/home/natalie/Sharedata/Visualization/Xcrysden/xcrysden-1.5.53/external/include > -c gl2ps.c > gl2ps.c: In function ?gl2psPutPDFText?: > gl2ps.c:3416: error: ?M_PI? undeclared (first use in this function) > gl2ps.c:3416: error: (Each undeclared identifier is reported only once > gl2ps.c:3416: error: for each function it appears in.) > > I notice the M_Pi is defined in the subroutine shank_Hinv.c, but it > apparently does not know the value in gl2ps.c. Thanks in advance for any > suggestions on how to fix this problem. > Sincerely, > Natalie Holzwarth > > > N. A. W. Holzwarth email: > natalie at wfu.edu > Department of Physics web: > http://www.wfu.edu/~natalie > Wake Forest University phone: > 1-336-758-5510 > Winston-Salem, NC 27109 USA office: Rm. 300 Olin > Physical Lab > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20120618/a9960f61/attachment.htm From arshadfarhan at hotmail.com Thu Jun 21 04:28:54 2012 From: arshadfarhan at hotmail.com (=?iso-8859-6?B?5c3lzyDH0dTPIOHRzcfm?=) Date: Thu, 21 Jun 2012 11:28:54 +0900 Subject: [xcrysden] segmentation violation in 3D Fermi surface Message-ID: Dear XCrysden Users, i have been facing a problem in viewing 3D fermi surface.the problem/error is same as discussed in this thread : http://www.democritos.it/pipermail/xcrysden/2010-May/000787.htmlaccording to this thread, lower of k points enables to visualize but i'm only using 300 kpoints .please guide me through the problem.regards,M. Arshad Farhan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20120621/a7bdfa40/attachment.htm From tone.kokalj at ijs.si Fri Jun 22 11:55:02 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 22 Jun 2012 11:55:02 +0200 Subject: [xcrysden] Difficulty compiling Xcrysden 1.5.53 In-Reply-To: References: Message-ID: <1340358902.31148.6.camel@catalyst.ijs.si> On Fri, 2012-06-15 at 18:29 -0400, Holzwarth, Natalie wrote: > Dear Xcrysden developers, > In compiling the 1.5.53 version of Xcrysden I ran into the > following error which was generated in ubuntu 10.4 and 12.04 using the > gcc compiler. I briefly scanned the archive and could not find > previous instances of this problem. > > > gcc -g -static -ansi -ffast-math -funroll-loops -DUSE_FONTS -pedantic > -Wall -DUSE_FONTS > -I/home/natalie/Sharedata/Visualization/Xcrysden/xcrysden-1.5.53/external/src/tcl8.5.11/generic -I/home/natalie/Sharedata/Visualization/Xcrysden/xcrysden-1.5.53/external/src/tk8.5.11/generic -I/home/natalie/Sharedata/Visualization/Xcrysden/xcrysden-1.5.53/external/include -c gl2ps.c > gl2ps.c: In function ?gl2psPutPDFText?: > gl2ps.c:3416: error: ?M_PI? undeclared (first use in this function) The problem with this M_PI is that its definition is not a C-standard, yet for long time it used to be defined in math.h. Seems that its definition is omitted in some new linux versions. The fix is very easy, though: whenever you encounter this compilation problem add the following line somewhere around the beginning of the respective file (in your case gl2ps.c): #define M_PI 3.14159265358979323846 This problem will be fixed in new version of xcrysden by hardocind the M_PI definition. Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From tone.kokalj at ijs.si Fri Jun 22 12:00:07 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 22 Jun 2012 12:00:07 +0200 Subject: [xcrysden] << Installing XCrysDen in CentOS 5.8 64bits >> In-Reply-To: References: Message-ID: <1340359207.31148.11.camel@catalyst.ijs.si> On Wed, 2012-06-13 at 18:29 -0300, I. Camps wrote: > Dear XCrysDen users, > > I am trying to install XCrysDen in CentOS 5.8 64bits unsuccessfully. > > I downloaded all the 1.5 shared and semishared versions. Also, I tried > to compiled from source. > > In all cases, there is always a library that is not in my system and > whenever I look for it, it is not available to my system version. Without providing more specific description of problem, nobody can help. Be more specific of encountered errors with a given xcrysden version. For example, what happen during the compilation, etc. Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From tone.kokalj at ijs.si Fri Jun 22 12:23:15 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 22 Jun 2012 12:23:15 +0200 Subject: [xcrysden] how to render pre-calculted 3D electron density for Wien2K in Xcrysden? In-Reply-To: <201206141657205155941@blem.ac.cn> References: <201206141657205155941@blem.ac.cn> Message-ID: <1340360595.31148.19.camel@catalyst.ijs.si> On Thu, 2012-06-14 at 16:57 +0800, ZhenChen wrote: > Dear xcrysden users, > > I have a question about wien2k electron density plot. > > As I know, we can use xcrysden to plot precalculated 2D electron > density and to render and calculate 3D electron density using 'x > -lapw5' command simutaneously. > > I am eager to know if it is convenient to render pre-calculated 3D > electron density? In my case, I use Wien2k to calculate electron > density in a supercomputer center and plot it in my personal computer, > so I can't calculate electron density in my computer where the > xcrysden runs. Unfortunately, there is no direct of way of doing this by xcrysden. You can, however, calculate a series of 2D slices on a supercomputer and then concatenate the *.rho files into a 3D XSF file, which can then be used on a local machine. You may find it convenient to write a few scripts to automate this *.rho --> XSF process. > What should I modify about the commands? Do I have to write a whole > new script? What files do I have to get before a plot? If you know a bit about the Tcl syntax you may look into the wnMakeIn5_2D3D procedure which is located in Tcl/wnDensity.tcl file. This is the proc that do the "3D" job. There you may see how the *.in5 files are generated and how the resulting *.rho files are transformed into XSF format. Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From tone.kokalj at ijs.si Fri Jun 22 12:27:59 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 22 Jun 2012 12:27:59 +0200 Subject: [xcrysden] segmentation violation in 3D Fermi surface In-Reply-To: References: Message-ID: <1340360879.31148.22.camel@catalyst.ijs.si> On Thu, 2012-06-21 at 11:28 +0900, ???? ???? ????? wrote: > Dear XCrysden Users, > i have been facing a problem in viewing 3D fermi surface. > the problem/error is same as discussed in this > thread : http://www.democritos.it/pipermail/xcrysden/2010-May/000787.html > according to this thread, lower of k points enables to visualize but > i'm only using 300 kpoints . > please guide me through the problem. I believe it is you who should guide us through your problem. Is the above stated thread the correct one? If so I cannot understand your problem. Be more specific. Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From zchen at blem.ac.cn Sat Jun 23 10:03:21 2012 From: zchen at blem.ac.cn (ZhenChen) Date: Sat, 23 Jun 2012 16:03:21 +0800 Subject: [xcrysden] how to render pre-calculted 3D electron Message-ID: <201206231603214566797@blem.ac.cn> Dear Anton, Thank you very much for your suggestions. I will struggle to solve this problem. If I have any progress, I would like to have you know and share to all xcrysden users. Best regards, Zhen Chen 2012-06-23 ------------------------------ ?? PhD. candidate Zhen Chen ------------------------------ Prof. Jianqi Li's group, A06 Beijing Laboratory of Electron Microscopy Institute of Physics Chinese Academy of Sciences P. O. Box 603 Beijing 100190, China Tel: 86-10-82648001 URL: http://www.blem.ac.cn/english/study-A06-1.asp ????????zchen at blem.ac.cn Date: Fri, 22 Jun 2012 12:23:15 +0200 From: Tone Kokalj Subject: Re: [xcrysden] how to render pre-calculted 3D electron density for Wien2K in Xcrysden? To: xcrysden at democritos.it Message-ID: <1340360595.31148.19.camel at catalyst.ijs.si> Content-Type: text/plain; charset="UTF-8" On Thu, 2012-06-14 at 16:57 +0800, ZhenChen wrote: > Dear xcrysden users, > > I have a question about wien2k electron density plot. > > As I know, we can use xcrysden to plot precalculated 2D electron > density and to render and calculate 3D electron density using 'x > -lapw5' command simutaneously. > > I am eager to know if it is convenient to render pre-calculated 3D > electron density? In my case, I use Wien2k to calculate electron > density in a supercomputer center and plot it in my personal computer, > so I can't calculate electron density in my computer where the > xcrysden runs. Unfortunately, there is no direct of way of doing this by xcrysden. You can, however, calculate a series of 2D slices on a supercomputer and then concatenate the *.rho files into a 3D XSF file, which can then be used on a local machine. You may find it convenient to write a few scripts to automate this *.rho --> XSF process. > What should I modify about the commands? Do I have to write a whole > new script? What files do I have to get before a plot? If you know a bit about the Tcl syntax you may look into the wnMakeIn5_2D3D procedure which is located in Tcl/wnDensity.tcl file. This is the proc that do the "3D" job. There you may see how the *.in5 files are generated and how the resulting *.rho files are transformed into XSF format. Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20120623/f959afa5/attachment.htm From martin at ruby.chemie.uni-freiburg.de Sat Jun 23 18:32:08 2012 From: martin at ruby.chemie.uni-freiburg.de (Martin Kroeker) Date: Sat, 23 Jun 2012 18:32:08 +0200 (CEST) Subject: [xcrysden] how to render pre-calculated 3D electron density for Wien2K in xcrysden Message-ID: <20120623163208.25ECA801B3@ruby.chemie.uni-freiburg.de> Get Masao Arai's wien2venus script (you will find it linked in the unsupported/contributed software section of the wien2k website). This already automates the calculation and combination of the stack of 2D slices - you then only need to reaarange its output into XSF format.(Or use either VENUS or DRAWxtl to view the "rho3d" data it creates). -- Dr. Martin Kroeker martin at ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg From arshadfarhan at hotmail.com Tue Jun 26 04:57:55 2012 From: arshadfarhan at hotmail.com (=?iso-8859-6?B?5c3lzyDH0dTPIOHRzcfm?=) Date: Tue, 26 Jun 2012 11:57:55 +0900 Subject: [xcrysden] segmentation violation in 3D Fermi surface In-Reply-To: <1340360879.31148.22.camel@catalyst.ijs.si> References: , <1340360879.31148.22.camel@catalyst.ijs.si> Message-ID: Dear prof. Tone,yes this thread is correct. i am trying to calculate the fermi surface for a non magnetic case by Wien2k & it's showing this error "Child Killed: segmentation violation". (i prefer to use terminal mode) i should mention here that i'm using the latest version of XCrysden and that for some other magnetic materials , it worked great.although i had tried by reducing the k-points by which, according to this thread, i could visualize FS but i got same error.Regards,M. Arshad Farhan > From: tone.kokalj at ijs.si > To: xcrysden at democritos.it > Date: Fri, 22 Jun 2012 12:27:59 +0200 > Subject: Re: [xcrysden] segmentation violation in 3D Fermi surface > > On Thu, 2012-06-21 at 11:28 +0900, ???? ???? ????? wrote: > > Dear XCrysden Users, > > i have been facing a problem in viewing 3D fermi surface. > > the problem/error is same as discussed in this > > thread : http://www.democritos.it/pipermail/xcrysden/2010-May/000787.html > > according to this thread, lower of k points enables to visualize but > > i'm only using 300 kpoints . > > please guide me through the problem. > > I believe it is you who should guide us through your problem. > Is the above stated thread the correct one? > If so I cannot understand your problem. Be more specific. > > Regards, Tone > > -- > Anton Kokalj > J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia > (tel: +386-1-477-3523 // fax:+386-1-477-3822) > > Please, if possible, avoid sending me Word or PowerPoint attachments. > See: http://www.gnu.org/philosophy/no-word-attachments.html > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20120626/479cc695/attachment.htm From john.tse at usask.ca Tue Jun 26 13:20:08 2012 From: john.tse at usask.ca (Tse, John) Date: Tue, 26 Jun 2012 11:20:08 +0000 Subject: [xcrysden] XCrySDen Digest, Vol 53, Issue 9 In-Reply-To: References: Message-ID: <9A168A40-D58D-49D8-9548-3F621F48093C@mail.usask.ca> Dear Eileen I will attend the morning session of the conference. Then I will drive to the airport and take the 4 pm flight to Washington. I will contact you there. Love John Sent from my iPad On 2012-06-26, at 1:57 AM, wrote: > Send XCrySDen mailing list submissions to > xcrysden at democritos.it > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/xcrysden > or, via email, send a message with subject or body 'help' to > xcrysden-request at democritos.it > > You can reach the person managing the list at > xcrysden-owner at democritos.it > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of XCrySDen digest..." > > > Today's Topics: > > 1. Re: segmentation violation in 3D Fermi surface (???? ???? ?????) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 26 Jun 2012 11:57:55 +0900 > From: ???? ???? ????? > Subject: Re: [xcrysden] segmentation violation in 3D Fermi surface > To: Xcrysden mailing list > Message-ID: > Content-Type: text/plain; charset="iso-8859-6" > > > Dear prof. Tone,yes this thread is correct. i am trying to calculate the fermi surface for a non magnetic case by Wien2k & it's showing this error "Child Killed: segmentation violation". (i prefer to use terminal mode) i should mention here that i'm using the latest version of XCrysden and that for some other magnetic materials , it worked great.although i had tried by reducing the k-points by which, according to this thread, i could visualize FS but i got same error.Regards,M. Arshad Farhan > >> From: tone.kokalj at ijs.si >> To: xcrysden at democritos.it >> Date: Fri, 22 Jun 2012 12:27:59 +0200 >> Subject: Re: [xcrysden] segmentation violation in 3D Fermi surface >> >> On Thu, 2012-06-21 at 11:28 +0900, ???? ???? ????? wrote: >>> Dear XCrysden Users, >>> i have been facing a problem in viewing 3D fermi surface. >>> the problem/error is same as discussed in this >>> thread : http://www.democritos.it/pipermail/xcrysden/2010-May/000787.html >>> according to this thread, lower of k points enables to visualize but >>> i'm only using 300 kpoints . >>> please guide me through the problem. >> >> I believe it is you who should guide us through your problem. >> Is the above stated thread the correct one? >> If so I cannot understand your problem. Be more specific. >> >> Regards, Tone >> >> -- >> Anton Kokalj >> J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia >> (tel: +386-1-477-3523 // fax:+386-1-477-3822) >> >> Please, if possible, avoid sending me Word or PowerPoint attachments. >> See: http://www.gnu.org/philosophy/no-word-attachments.html >> >> _______________________________________________ >> XCrySDen mailing list >> XCrySDen at democritos.it >> http://www.democritos.it/mailman/listinfo/xcrysden > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/xcrysden/attachments/20120626/479cc695/attachment-0001.htm > > ------------------------------ > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > > > End of XCrySDen Digest, Vol 53, Issue 9 > ***************************************