From owner-chemistry@ccl.net Fri May 26 15:36:00 2017 From: "Sergio Emanuel Galembeck segalemb ~~ usp.br" To: CCL Subject: CCL: graphene workshop in Brazil Message-Id: <-52814-170526064548-11429-iDwhpjLhhjG4vdjdCiWwBw%a%server.ccl.net> X-Original-From: Sergio Emanuel Galembeck Content-Type: multipart/alternative; boundary="Apple-Mail=_18B423A9-9CA1-4436-97C0-AFB021D5A02E" Date: Fri, 26 May 2017 07:45:36 -0300 Mime-Version: 1.0 (Mac OS X Mail 10.3 \(3273\)) Sent to CCL by: Sergio Emanuel Galembeck [segalemb() usp.br] --Apple-Mail=_18B423A9-9CA1-4436-97C0-AFB021D5A02E Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Dear colleagues, =46rom December 11 to 14, 2017, the 3rd School of Computational = Chemistry - Theory of new materials at atomistic level: Graphene, = Graphene Defects and =CF=80-Conjugated Polyradical Systems will be held = at the Department of Chemistry of FFCLRP-USP, in Ribeirao Preto, SP, = Brazil. This event will be organized in form of lectures given by = theoretical and experimental specialists from Brazil and abroad. The = objective of this workshop is to present an overview of different = computational methods and experimental techniques to study graphene, = graphene defects and polyradicaloids, as well as to discuss outstanding = applications. There will be a session for oral presentations of selected = works, and also a poster session. Registration will be open from July 15 to August 14, and 80 places will = be available. More information can be found at: = http://3qc.iqm.unicamp.br/EQC Ribeirao Preto is a medium-sized Brazilian city, situated in the Sao = Paulo State, 300 km from Sao Paulo City. This city has a large number of = science and technology groups, especially at the University of Sao Paulo = campus. Ribeirao Preto is also one of the most important agrobusiness = centers in Brazil.=20 Best regards, Sergio Emanuel Galembeck= --Apple-Mail=_18B423A9-9CA1-4436-97C0-AFB021D5A02E Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8 =09 =09 =09

Dear = colleagues,

=46rom December 11 to 14, 2017, the = 3rd School of Computational Chemistry - Theory of = new materials at atomistic level: Graphene, Graphene Defects and = =CF=80-Conjugated = Polyradical Systems will be held at the Department of Chemistry of FFCLRP-USP, in = Ribeirao Preto, SP, Brazil. This event will be organized in form of lectures given by theoretical and = experimental specialists from Brazil and abroad. The objective of this workshop is to present an = overview of different computational methods and experimental techniques to study graphene, = graphene defects and polyradicaloids, as well as to discuss outstanding applications. There = will be a session for oral presentations of selected works, and also a poster session.

Registration will be open from July 15 to August = 14, and 80 places will be available. More information can be found at: http://3qc.iqm.unicamp.br/EQC

Ribeirao Preto is a medium-sized = Brazilian city, situated in the Sao Paulo State, 300 km from Sao Paulo City. This city has a large number of science and technology = groups, especially at the University of Sao Paulo campus. Ribeirao Preto is also one of the most = important agrobusiness centers in Brazil.

Best = regards,

Sergio = Emanuel Galembeck

= --Apple-Mail=_18B423A9-9CA1-4436-97C0-AFB021D5A02E-- From owner-chemistry@ccl.net Fri May 26 16:11:00 2017 From: "Igors Mihailovs igorsm*cfi.lu.lv" To: CCL Subject: CCL:G: IAtGet: Unknown atom type problem in Gaussian (solved) Message-Id: <-52815-170526121616-28656-I0OKnpC0LdcY3san74i5uA^_^server.ccl.net> X-Original-From: Igors Mihailovs Content-Type: multipart/alternative; boundary="------------A69E2D86F9BB07C6BE6D3035" Date: Fri, 26 May 2017 19:17:46 +0300 MIME-Version: 1.0 Sent to CCL by: Igors Mihailovs [igorsm||cfi.lu.lv] This is a multi-part message in MIME format. --------------A69E2D86F9BB07C6BE6D3035 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit Dear all, I am writing to share my little experience because there is almost nothing about this problem on the Internet (at least if one uses /Google/™). Sorry if this seems like an explanation for kids for You; it's just the style I myself understand the best :-) Description for the ADMP keyword states that /most jobs will not require [additional input]/. And yet if you have some additional input with /*lower*/ priority than it would be for ADMP, the job dies and the following error appears: *IAtGet: Unknown atom type* Considering that lower priority: look up the very beginning of the /Gaussian NN Reference/ or go here (on the /Gaussian/ homepage). For example, * additional input for Opt=ModRedundant or CPHF=RdFreq is of /higher/ priority than the one for ADMP, while the * additional input for SCRF=Read or basis set specifications for the Gen keyword are of /lower/ priority than the input for ADMP. Actually, there is a hint on the mentioned pages of the /Reference –/ the keyword field reads: /*ADMP* and *BOMD* _required_ input and *ReadVelocity*, *ReadMWVelocity* options/, so we can actually figure out that there /is/ some required input for ADMP, just like in the case of BOMD. The solution is incredibly simple: you just have to add a blank line between the sections of additional input, the last one of higher priority and the first one with lower priority than the one of ADMP. For example, instead of %Mem=120GB %NProcShared=16 %Chk=/home/igors/darba/IN_dihedral_ADMP_DL1.chk #T MaxDisk=250GB CAM-B3LYP/6-311G(d,p) ADMP=(MaxPoints=10000) Geom=(Crowd,ModRedundant) Guess=Mix scrf=(cpcm,solvent=Acetonitrile,Read) ::: IN17_469_CAM_6311_acetonitr_SASdrc_xplc_90deg IN17_469_CAM_6311_acetonitr_SASdrc_xplc_90deg GeometryOptimization Admp ADMP 1 0 1 C 3.440990 2.083690 -0.808840 C 3.774870 0.798710 -0.409860 C 2.843130 -0.009000 0.245700 D 8 9 11 12 F Surface=SAS Dis Rep Cav you should have %Mem=120GB %NProcShared=16 %Chk=/home/igors/darba/IN_dihedral_ADMP_DL1.chk #T MaxDisk=250GB CAM-B3LYP/6-311G(d,p) ADMP=(MaxPoints=10000) Geom=(Crowd,ModRedundant) Guess=Mix scrf=(cpcm,solvent=Acetonitrile,Read) ::: IN17_469_CAM_6311_acetonitr_SASdrc_xplc_90deg IN17_469_CAM_6311_acetonitr_SASdrc_xplc_90deg GeometryOptimization Admp ADMP 1 0 1 C 3.440990 2.083690 -0.808840 C 3.774870 0.798710 -0.409860 C 2.843130 -0.009000 0.245700 D 8 9 11 12 F Surface=SAS Dis Rep Cav No more, no less. Everything goes on smoothly then. Actually, this is in full analogy with BOMD, which requires the number of dissociation paths in the additional input section, but accepts blank line instead of zero. *P.S.* If You are working with ADMP, I would be happy for comments like "why do you need those 10000 cycles". I have never dealt with ADMP before (at least not seriously), but I have heard form proteinist friends that one requires several nanoseconds for MD calculations to convege reliably, and one step in ADMP is just 0.1 fs… With best regards, Igors Mihailovs ISSP University of Latvia --------------A69E2D86F9BB07C6BE6D3035 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit Dear all,

I am writing to share my little experience because there is almost nothing about this problem on the Internet (at least if one uses Google™). Sorry if this seems like an explanation for kids for You; it's just the style I myself understand the best :-)

Description for the ADMP keyword states that most jobs will not require [additional input]. And yet if you have some additional input with lower priority than it would be for ADMP, the job dies and the following error appears:

IAtGet: Unknown atom type

Considering that lower priority: look up the very beginning of the Gaussian NN Reference or go here (on the Gaussian homepage). For example,

additional input for Opt=ModRedundant or CPHF=RdFreq is of higher priority than the one for ADMP, while the
additional input for SCRF=Read or basis set specifications for the Gen keyword are of lower priority than the input for ADMP.

Actually, there is a hint on the mentioned pages of the Reference – the keyword field reads:
ADMP and BOMD required input and ReadVelocity, ReadMWVelocity options,
so we can actually figure out that there is some required input for ADMP, just like in the case of BOMD.

The solution is incredibly simple: you just have to add a blank line between the sections of additional input, the last one of higher priority and the first one with lower priority than the one of ADMP. For example, instead of

%Mem=120GB
%NProcShared=16
%Chk=/home/igors/darba/IN_dihedral_ADMP_DL1.chk

#T MaxDisk=250GB CAM-B3LYP/6-311G(d,p) ADMP=(MaxPoints=10000) Geom=(Crowd,ModRedundant) Guess=Mix scrf=(cpcm,solvent=Acetonitrile,Read)

::: IN17_469_CAM_6311_acetonitr_SASdrc_xplc_90deg IN17_469_CAM_6311_acetonitr_SASdrc_xplc_90deg GeometryOptimization Admp ADMP 1

0 1
   C     3.440990    2.083690   -0.808840
   C     3.774870    0.798710   -0.409860
   C     2.843130   -0.009000    0.245700

D 8 9 11 12 F

Surface=SAS Dis Rep Cav

you should have

%Mem=120GB
%NProcShared=16

%Chk=/home/igors/darba/IN_dihedral_ADMP_DL1.chk

#T MaxDisk=250GB CAM-B3LYP/6-311G(d,p) ADMP=(MaxPoints=10000) Geom=(Crowd,ModRedundant) Guess=Mix scrf=(cpcm,solvent=Acetonitrile,Read)

::: IN17_469_CAM_6311_acetonitr_SASdrc_xplc_90deg IN17_469_CAM_6311_acetonitr_SASdrc_xplc_90deg GeometryOptimization Admp ADMP 1

0 1
   C     3.440990    2.083690   -0.808840
   C     3.774870    0.798710   -0.409860
   C     2.843130   -0.009000    0.245700

D 8 9 11 12 F

Surface=SAS Dis Rep Cav

No more, no less. Everything goes on smoothly then.

Actually, this is in full analogy with BOMD, which requires the number of dissociation paths in the additional input section, but accepts blank line instead of zero.

P.S. If You are working with ADMP, I would be happy for comments like "why do you need those 10000 cycles". I have never dealt with ADMP before (at least not seriously), but I have heard form proteinist friends that one requires several nanoseconds for MD calculations to convege reliably, and one step in ADMP is just 0.1 fs…

With best regards,
Igors Mihailovs
ISSP University of Latvia --------------A69E2D86F9BB07C6BE6D3035--