An introductory tutorial on how to use the constrained density functional theory (CDFT) module in the CP2K open-source quantum chemistry and solid state physics software package. The talk was given at the CP2K UK User meeting on January 12, 2018, at the University of Lincoln.
e-content of Stereochemistry for Pharmacy and Chemistry students.
contents includes Isomerism, Chirality, Stereoisomers, Enantiomer, Diastereomer, Cis And Trans Configuration ,L And D Configuration ,R And S Configuration and Importance of the chirality in drugs ,Intravenous anaesthetics , etc.
The document discusses four plants used in traditional Indian medicine to treat diabetes: Gymnema sylvestre, Salacia reticulata, Pterocarpus marsupium, and Swertia chirata. It describes the chemical constituents of each plant including major components like gymnemic acid, salacinol, and mangiferin. It also summarizes the proposed mechanisms of action for lowering blood glucose, such as inhibiting alpha-glucosidase enzymes and increasing insulin secretion. A brief overview of other medicinal uses and potential side effects is provided for each plant.
B. Sc. Sem - I Unit-IV (D) Orientation by Dr Pramod R Padolepramod padole
ย
Orientation: Effect of substituent groups. Activating and deactivating groups. Theory of reactivity and orientation on the basis of inductive and resonance effects (-CH3, -OH, -NO2 and โCl groups).
This document discusses various types of organic reactions including ionic reactions, radical reactions, and nucleophilic substitution reactions. It provides details on:
1) The mechanisms of SN1 and SN2 reactions including rate laws, stereochemistry, substrate structure effects, and effects of nucleophiles, leaving groups, and solvents. SN1 reactions proceed through a carbocation intermediate and follow first-order kinetics while SN2 reactions are bimolecular.
2) Substrate structures that favor SN1 or SN2 reactions. Tertiary substrates favor SN1 while primary and secondary favor SN2. Allylic and benzylic compounds are more reactive in both SN1 and SN2 reactions.
3)
1) Chiral molecules can undergo three types of reactions at the chiral center: inversion, retention, and racemization. Inversion changes the configuration, retention keeps it the same, and racemization converts an enantiomer to a racemic mixture.
2) Racemization is the process of converting an optically active compound into a racemic mixture. It can occur through mechanisms like anion formation, thermal reactions, or reversible intermediate formation. Racemic mixtures contain equal amounts of both enantiomers and are optically inactive.
3) Resolution is the separation of a racemic mixture into its pure enantiomers, often by converting them into diastereomers with different properties like crystallization or
IB Chemistry on Standard Reduction Potential, Standard Hydrogen Electrode and...Lawrence kok
ย
The document discusses standard electrode potentials and how they are measured. It explains that the standard hydrogen electrode is used as a reference with a potential of 0 V. Other half-cell potentials are measured against this to determine their standard electrode potential. Common half-cells include metal/metal ion, gas/ion, and ion/ion systems. Standard conditions of 1 M concentrations, 1 atm pressure, and 298K temperature must be used. The potentials of zinc/zinc ion, iron III/iron II, and chlorine/chloride ion half-cells are given as examples.
This document discusses flavonoids, which are polyphenolic compounds found in plants. It provides an introduction to flavonoids, including their structure, occurrence in plants, and functions. It also describes methods for isolating, extracting, and determining the structures of flavonoids, such as using chromatography, ultraviolet and infrared spectroscopy, and nuclear magnetic resonance spectroscopy. Key tests for detecting flavonoids include the Shinoda test and sodium hydroxide test.
- Developed syllabus and lesson plans for weekly 2-hour tutorials
- Led discussions on assigned readings and provided feedback on student papers
- Graded assignments and exams
Harvard University Cambridge, MA
Research Assistant to Professor X. Xxxxx Sept 2011 - May 2012
- Conducted archival research and interviews on the history of science and technology policy in Japan
- Analyzed data and assisted with writing and editing of scholarly publications
- Presented research findings at national conferences
University of California-Berkeley Berkeley, CA
Teaching Assistant: Cultural Anthropology Jan 2010 - May 2010
- Held weekly discussion sections and office hours for 80 undergraduate students
- Graded assignments, papers, and exams
RE
e-content of Stereochemistry for Pharmacy and Chemistry students.
contents includes Isomerism, Chirality, Stereoisomers, Enantiomer, Diastereomer, Cis And Trans Configuration ,L And D Configuration ,R And S Configuration and Importance of the chirality in drugs ,Intravenous anaesthetics , etc.
The document discusses four plants used in traditional Indian medicine to treat diabetes: Gymnema sylvestre, Salacia reticulata, Pterocarpus marsupium, and Swertia chirata. It describes the chemical constituents of each plant including major components like gymnemic acid, salacinol, and mangiferin. It also summarizes the proposed mechanisms of action for lowering blood glucose, such as inhibiting alpha-glucosidase enzymes and increasing insulin secretion. A brief overview of other medicinal uses and potential side effects is provided for each plant.
B. Sc. Sem - I Unit-IV (D) Orientation by Dr Pramod R Padolepramod padole
ย
Orientation: Effect of substituent groups. Activating and deactivating groups. Theory of reactivity and orientation on the basis of inductive and resonance effects (-CH3, -OH, -NO2 and โCl groups).
This document discusses various types of organic reactions including ionic reactions, radical reactions, and nucleophilic substitution reactions. It provides details on:
1) The mechanisms of SN1 and SN2 reactions including rate laws, stereochemistry, substrate structure effects, and effects of nucleophiles, leaving groups, and solvents. SN1 reactions proceed through a carbocation intermediate and follow first-order kinetics while SN2 reactions are bimolecular.
2) Substrate structures that favor SN1 or SN2 reactions. Tertiary substrates favor SN1 while primary and secondary favor SN2. Allylic and benzylic compounds are more reactive in both SN1 and SN2 reactions.
3)
1) Chiral molecules can undergo three types of reactions at the chiral center: inversion, retention, and racemization. Inversion changes the configuration, retention keeps it the same, and racemization converts an enantiomer to a racemic mixture.
2) Racemization is the process of converting an optically active compound into a racemic mixture. It can occur through mechanisms like anion formation, thermal reactions, or reversible intermediate formation. Racemic mixtures contain equal amounts of both enantiomers and are optically inactive.
3) Resolution is the separation of a racemic mixture into its pure enantiomers, often by converting them into diastereomers with different properties like crystallization or
IB Chemistry on Standard Reduction Potential, Standard Hydrogen Electrode and...Lawrence kok
ย
The document discusses standard electrode potentials and how they are measured. It explains that the standard hydrogen electrode is used as a reference with a potential of 0 V. Other half-cell potentials are measured against this to determine their standard electrode potential. Common half-cells include metal/metal ion, gas/ion, and ion/ion systems. Standard conditions of 1 M concentrations, 1 atm pressure, and 298K temperature must be used. The potentials of zinc/zinc ion, iron III/iron II, and chlorine/chloride ion half-cells are given as examples.
This document discusses flavonoids, which are polyphenolic compounds found in plants. It provides an introduction to flavonoids, including their structure, occurrence in plants, and functions. It also describes methods for isolating, extracting, and determining the structures of flavonoids, such as using chromatography, ultraviolet and infrared spectroscopy, and nuclear magnetic resonance spectroscopy. Key tests for detecting flavonoids include the Shinoda test and sodium hydroxide test.
- Developed syllabus and lesson plans for weekly 2-hour tutorials
- Led discussions on assigned readings and provided feedback on student papers
- Graded assignments and exams
Harvard University Cambridge, MA
Research Assistant to Professor X. Xxxxx Sept 2011 - May 2012
- Conducted archival research and interviews on the history of science and technology policy in Japan
- Analyzed data and assisted with writing and editing of scholarly publications
- Presented research findings at national conferences
University of California-Berkeley Berkeley, CA
Teaching Assistant: Cultural Anthropology Jan 2010 - May 2010
- Held weekly discussion sections and office hours for 80 undergraduate students
- Graded assignments, papers, and exams
RE
Drug resistance arises when microbes such as bacteria, viruses, and fungi develop the ability to survive and grow in the presence of a drug that would normally kill them. There are several mechanisms by which drug resistance can develop, including alterations to drug targets, increased drug efflux, and enhanced drug inactivation. In cancer specifically, drug resistance is a major challenge in chemotherapy and can develop through changes to drug targets, increased DNA repair, or defective apoptosis pathways. Overcoming drug resistance requires strategies like pharmacokinetic monitoring, pharmacogenetic testing, and developing new targeted therapies.
This document discusses stereochemistry and chirality in drug molecules. It defines stereoisomers as molecules with the same bonding but different spatial arrangements, and enantiomers as two stereoisomers that are mirror images of each other. Chiral drugs can exist as single enantiomers or as racemic mixtures of both. Using single enantiomers is preferable since biological interactions may differ for each form. The document provides examples of naming enantiomers and determining chirality and stereoisomers in molecules.
Phyllanthus niruri is a small herb used in indigenous medicine systems to treat liver dysfunction. It contains several active constituents like lignans, flavonoids, and tannins that have been shown to protect the liver from damage caused by toxins, drugs, and viruses. Studies demonstrate that extracts of P. niruri can reduce elevated liver enzymes and protect liver cells induced by chemicals like carbon tetrachloride, galactosamine, and paracetamol overdose. The primary active constituents, phyllanthin and hypophyllanthin, have hepatoprotective and antioxidant properties. P. niruri is considered effective for treating liver diseases and injuries based on its long traditional use and
Salacia reticulata is a plant that grows in South Asia and contains compounds that have antidiabetic properties. It contains mangiferin, kotalanol, salacinol, and 13-MRT, which are responsible for its antidiabetic effects. Mangiferin has been shown to inhibit the protein tyrosine phosphatase 1B, which plays a role in diabetes treatment. Kotalanol and salacinol are potent alpha-glucosidase inhibitors. Consuming Salacia tea or extracts with meals has been shown to lower blood sugar levels and hemoglobin A1C in people with type 2 diabetes. Salacia reticulata is used in Ayurvedic medicine for
The document discusses coumarins, which are naturally occurring compounds with diverse pharmacological properties. Coumarins are found in many plant species and have a wide range of biological activities. Some examples mentioned include uses as anticoagulants, antimicrobials, anti-inflammatories, and more. Common coumarin derivatives discussed include warfarin and various synthetic routes for producing coumarins are also summarized such as the Perkin reaction and Pechmann condensation.
The document discusses the Knorr pyrazole synthesis reaction which converts hydrazines or derivatives and 1,3-dicarbonyl compounds to pyrazoles using an acid catalyst. The mechanism involves acid-catalyzed imine formation on either carbonyl carbon, followed by attack of the other nitrogen on the other carbonyl group. This forms a diimine compound which deprotonates to generate the final pyrazole product. Several examples of pyrazoles synthesized using this reaction are mentioned, including antipyrine, celecoxib, and metamizole sodium which have various medical applications.
1. Alkaloids are basic nitrogenous plant compounds that contain heterocyclic rings. They are classified based on the heterocyclic ring present and have pharmacological activity.
2. Coniine is a colorless, toxic alkaloid found in hemlock seeds. It contains a piperidine ring and was used to kill Socrates. Its structure was determined to be hexahydroconyrine.
3. Piperine is a weak base found in black pepper. It contains a piperidine group joined to piperic acid, which has a side chain containing two carbon-carbon double bonds and a carboxyl group. Its structure was elucidated through chemical reactions.
The presentation is prepared for lecture for the M. Sc Chemistry students studying under University of Madras (MER3A: Unit III). It is dealing with Aromaticity and Organic Photochemistry
The document discusses the Diels-Alder reaction, which involves a diene reacting with a dienophile to form a six-membered ring. Key characteristics include versatility, stereoselectivity, and reversibility. The mechanism involves overlap of the HOMO of the diene and LUMO of the dienophile. The stereochemistry of products is governed by the cis principle and endo rule. Variations include retro Diels-Alder reactions and cycloadditions involving allyl cations/anions.
1. Zingiberene is a turmerone-type compound found in turmeric root, essential oil, and dried rhizome. It is a sesquiterpenoid with three consecutive isoprene units.
2. Natural sources containing zingiberene include turmeric, ginger, sage, aralia, and angelica roots.
3. Zingiberene has potential antioxidant, anti-inflammatory, anti-tumour and anti-microbial properties. It may help fight infections and protect against stomach ulcers.
The document discusses several heterocyclic compounds including quinolines, isoquinolines, and indoles. It summarizes key reactions used to synthesize these compounds, including the Combes, Friedlander, Knorr, and Skraup reactions for quinoline synthesis. It also discusses the Bischler-Napieralski, Pictet-Spengler, and Pomeranz-Fritsch reactions for isoquinoline synthesis and the Fischer, Madelung, and Reissert reactions for indole synthesis, along with mechanisms and examples of each reaction. Reactivity and substitution patterns are also covered for quinolines, isoquinolines and indoles.
There are several approaches to drug discovery including modifying known molecules, combining drugs, screening natural sources, identifying new drug targets, and rational drug design. A lead compound is used as a starting point for optimization. Databases contain chemical compounds that can be searched to find potential drug candidates. Structure-based drug design uses the 3D structure of the target to search databases and design new molecules. De novo drug design involves determining the target structure and designing new molecules without existing leads through molecular modeling and computer programs.
The document describes the synthesis of several drugs including ketoconazole, metronidazole, miconazole, celecoxib, metamizole sodium, terconazole, alprazolam, triamtrene, sulfamerazine, trimethoprim, hydroxychloroquine, quinine, chloroquine, quinacrine, amsacrine, prochlorperazine, promazine, chlorpromazine, and theophylline. The syntheses involve multiple reaction steps starting with various reagents and intermediates to ultimately form the target drug molecule through condensation, reduction, oxidation, hydrolysis, and other organic reactions.
Active constituent of Phyllanthus niruri for liver dysfunctionASHOK GAUTAM
ย
Phyllanthus niruri is a plant found throughout India that contains lignans including phyllanthin and hypophyllanthin. These compounds have been shown to inhibit hepatitis B virus by blocking the viral DNA polymerase enzyme and binding to the hepatitis B surface antigen. The extraction process involves placing powdered P. niruri leaves in methanol for 24 hours using a Soxhlet apparatus to extract the phyllanthin, which is then analyzed using HPLC. P. niruri has several potential medical uses due to its antioxidant, antimicrobial, anti-inflammatory, blood sugar lowering, and kidney stone preventing properties.
O documento discute os hidrocarbonetos, incluindo suas classificaรงรตes, fontes, usos e processos de refino. ร descrito o gรกs natural, sua composiรงรฃo, distribuiรงรฃo e uso no Brasil.
This document summarizes the structural elucidation of camphor. Camphor is derived from camphor laurel trees and has the molecular formula C10H16O. It contains a bicyclic ring system and a ketone group. Through various chemical reactions and oxidations, it was determined that camphor contains a six-membered ring with methyl substituents and a ketone carbonyl group. Oxidation of camphor produces camphoric acid and camphoronic acid, allowing elucidation of camphor's carbon frame structure.
IRJET- A New Approach to Economic Load Dispatch by using Improved QEMA ba...IRJET Journal
ย
This document proposes an improved Quantum behaved electro-magnetism algorithm particle swarm optimization (QEMAPSO) approach to solve the economic load dispatch (ELD) problem. The objective is to minimize the total generation cost while considering constraints like generator limits, transmission losses, and valve point effects. It formulates the ELD problem and describes the QEMA-PSO algorithm which uses QEMA to determine an initial solution that is then optimized using PSO. Results on a 6-generator IEEE 30-bus test system show that the proposed QEMA-PSO approach improves upon other methods like genetic algorithm and dance bee colony optimization in minimizing costs and emissions.
The document summarizes research on photoferroic materials for solar cell applications. It discusses computational studies of the electronic and optical properties of three candidate photoferroic minerals: enargite, stephanite, and bournonite. The studies show they have suitable bandgaps and absorption properties. Rashba splitting was also found in bournonite. The document then discusses how defects could be tolerated in these materials through shallow defect levels related to their electronic structure. Finally, methods for further computational investigation of defects and spontaneous polarization are presented.
Drug resistance arises when microbes such as bacteria, viruses, and fungi develop the ability to survive and grow in the presence of a drug that would normally kill them. There are several mechanisms by which drug resistance can develop, including alterations to drug targets, increased drug efflux, and enhanced drug inactivation. In cancer specifically, drug resistance is a major challenge in chemotherapy and can develop through changes to drug targets, increased DNA repair, or defective apoptosis pathways. Overcoming drug resistance requires strategies like pharmacokinetic monitoring, pharmacogenetic testing, and developing new targeted therapies.
This document discusses stereochemistry and chirality in drug molecules. It defines stereoisomers as molecules with the same bonding but different spatial arrangements, and enantiomers as two stereoisomers that are mirror images of each other. Chiral drugs can exist as single enantiomers or as racemic mixtures of both. Using single enantiomers is preferable since biological interactions may differ for each form. The document provides examples of naming enantiomers and determining chirality and stereoisomers in molecules.
Phyllanthus niruri is a small herb used in indigenous medicine systems to treat liver dysfunction. It contains several active constituents like lignans, flavonoids, and tannins that have been shown to protect the liver from damage caused by toxins, drugs, and viruses. Studies demonstrate that extracts of P. niruri can reduce elevated liver enzymes and protect liver cells induced by chemicals like carbon tetrachloride, galactosamine, and paracetamol overdose. The primary active constituents, phyllanthin and hypophyllanthin, have hepatoprotective and antioxidant properties. P. niruri is considered effective for treating liver diseases and injuries based on its long traditional use and
Salacia reticulata is a plant that grows in South Asia and contains compounds that have antidiabetic properties. It contains mangiferin, kotalanol, salacinol, and 13-MRT, which are responsible for its antidiabetic effects. Mangiferin has been shown to inhibit the protein tyrosine phosphatase 1B, which plays a role in diabetes treatment. Kotalanol and salacinol are potent alpha-glucosidase inhibitors. Consuming Salacia tea or extracts with meals has been shown to lower blood sugar levels and hemoglobin A1C in people with type 2 diabetes. Salacia reticulata is used in Ayurvedic medicine for
The document discusses coumarins, which are naturally occurring compounds with diverse pharmacological properties. Coumarins are found in many plant species and have a wide range of biological activities. Some examples mentioned include uses as anticoagulants, antimicrobials, anti-inflammatories, and more. Common coumarin derivatives discussed include warfarin and various synthetic routes for producing coumarins are also summarized such as the Perkin reaction and Pechmann condensation.
The document discusses the Knorr pyrazole synthesis reaction which converts hydrazines or derivatives and 1,3-dicarbonyl compounds to pyrazoles using an acid catalyst. The mechanism involves acid-catalyzed imine formation on either carbonyl carbon, followed by attack of the other nitrogen on the other carbonyl group. This forms a diimine compound which deprotonates to generate the final pyrazole product. Several examples of pyrazoles synthesized using this reaction are mentioned, including antipyrine, celecoxib, and metamizole sodium which have various medical applications.
1. Alkaloids are basic nitrogenous plant compounds that contain heterocyclic rings. They are classified based on the heterocyclic ring present and have pharmacological activity.
2. Coniine is a colorless, toxic alkaloid found in hemlock seeds. It contains a piperidine ring and was used to kill Socrates. Its structure was determined to be hexahydroconyrine.
3. Piperine is a weak base found in black pepper. It contains a piperidine group joined to piperic acid, which has a side chain containing two carbon-carbon double bonds and a carboxyl group. Its structure was elucidated through chemical reactions.
The presentation is prepared for lecture for the M. Sc Chemistry students studying under University of Madras (MER3A: Unit III). It is dealing with Aromaticity and Organic Photochemistry
The document discusses the Diels-Alder reaction, which involves a diene reacting with a dienophile to form a six-membered ring. Key characteristics include versatility, stereoselectivity, and reversibility. The mechanism involves overlap of the HOMO of the diene and LUMO of the dienophile. The stereochemistry of products is governed by the cis principle and endo rule. Variations include retro Diels-Alder reactions and cycloadditions involving allyl cations/anions.
1. Zingiberene is a turmerone-type compound found in turmeric root, essential oil, and dried rhizome. It is a sesquiterpenoid with three consecutive isoprene units.
2. Natural sources containing zingiberene include turmeric, ginger, sage, aralia, and angelica roots.
3. Zingiberene has potential antioxidant, anti-inflammatory, anti-tumour and anti-microbial properties. It may help fight infections and protect against stomach ulcers.
The document discusses several heterocyclic compounds including quinolines, isoquinolines, and indoles. It summarizes key reactions used to synthesize these compounds, including the Combes, Friedlander, Knorr, and Skraup reactions for quinoline synthesis. It also discusses the Bischler-Napieralski, Pictet-Spengler, and Pomeranz-Fritsch reactions for isoquinoline synthesis and the Fischer, Madelung, and Reissert reactions for indole synthesis, along with mechanisms and examples of each reaction. Reactivity and substitution patterns are also covered for quinolines, isoquinolines and indoles.
There are several approaches to drug discovery including modifying known molecules, combining drugs, screening natural sources, identifying new drug targets, and rational drug design. A lead compound is used as a starting point for optimization. Databases contain chemical compounds that can be searched to find potential drug candidates. Structure-based drug design uses the 3D structure of the target to search databases and design new molecules. De novo drug design involves determining the target structure and designing new molecules without existing leads through molecular modeling and computer programs.
The document describes the synthesis of several drugs including ketoconazole, metronidazole, miconazole, celecoxib, metamizole sodium, terconazole, alprazolam, triamtrene, sulfamerazine, trimethoprim, hydroxychloroquine, quinine, chloroquine, quinacrine, amsacrine, prochlorperazine, promazine, chlorpromazine, and theophylline. The syntheses involve multiple reaction steps starting with various reagents and intermediates to ultimately form the target drug molecule through condensation, reduction, oxidation, hydrolysis, and other organic reactions.
Active constituent of Phyllanthus niruri for liver dysfunctionASHOK GAUTAM
ย
Phyllanthus niruri is a plant found throughout India that contains lignans including phyllanthin and hypophyllanthin. These compounds have been shown to inhibit hepatitis B virus by blocking the viral DNA polymerase enzyme and binding to the hepatitis B surface antigen. The extraction process involves placing powdered P. niruri leaves in methanol for 24 hours using a Soxhlet apparatus to extract the phyllanthin, which is then analyzed using HPLC. P. niruri has several potential medical uses due to its antioxidant, antimicrobial, anti-inflammatory, blood sugar lowering, and kidney stone preventing properties.
O documento discute os hidrocarbonetos, incluindo suas classificaรงรตes, fontes, usos e processos de refino. ร descrito o gรกs natural, sua composiรงรฃo, distribuiรงรฃo e uso no Brasil.
This document summarizes the structural elucidation of camphor. Camphor is derived from camphor laurel trees and has the molecular formula C10H16O. It contains a bicyclic ring system and a ketone group. Through various chemical reactions and oxidations, it was determined that camphor contains a six-membered ring with methyl substituents and a ketone carbonyl group. Oxidation of camphor produces camphoric acid and camphoronic acid, allowing elucidation of camphor's carbon frame structure.
IRJET- A New Approach to Economic Load Dispatch by using Improved QEMA ba...IRJET Journal
ย
This document proposes an improved Quantum behaved electro-magnetism algorithm particle swarm optimization (QEMAPSO) approach to solve the economic load dispatch (ELD) problem. The objective is to minimize the total generation cost while considering constraints like generator limits, transmission losses, and valve point effects. It formulates the ELD problem and describes the QEMA-PSO algorithm which uses QEMA to determine an initial solution that is then optimized using PSO. Results on a 6-generator IEEE 30-bus test system show that the proposed QEMA-PSO approach improves upon other methods like genetic algorithm and dance bee colony optimization in minimizing costs and emissions.
The document summarizes research on photoferroic materials for solar cell applications. It discusses computational studies of the electronic and optical properties of three candidate photoferroic minerals: enargite, stephanite, and bournonite. The studies show they have suitable bandgaps and absorption properties. Rashba splitting was also found in bournonite. The document then discusses how defects could be tolerated in these materials through shallow defect levels related to their electronic structure. Finally, methods for further computational investigation of defects and spontaneous polarization are presented.
APPLICATION OF PARTICLE SWARM OPTIMIZATION TO MICROWAVE TAPERED MICROSTRIP LINEScseij
ย
This document discusses using Particle Swarm Optimization (PSO) to design a tapered microstrip transmission line to match an arbitrary load to a 50ฮฉ line. PSO was used to optimize the impedances of a three section tapered line to minimize reflections. Simulations found impedances that gave good matching at 5GHz. PSO converged to solutions in under 1000 iterations. This demonstrates PSO's effectiveness in solving multi-objective microwave engineering optimization problems.
Application of particle swarm optimization to microwave tapered microstrip linescseij
ย
Application of metaheuristic algorithms has been of continued interest in the field of electrical engineering
because of their powerful features. In this work special design is done for a tapered transmission line used
for matching an arbitrary real load to a 50ฮฉ line. The problem at hand is to match this arbitray load to 50
ฮฉ line using three section tapered transmission line with impedances in decreasing order from the load. So
the problem becomes optimizing an equation with three unknowns with various conditions. The optimized
values are obtained using Particle Swarm Optimization. It can easily be shown that PSO is very strong in
solving this kind of multiobjective optimization problems.
IRJET- Optimal Generation Scheduling for Thermal UnitsIRJET Journal
ย
This document summarizes a research paper that develops an optimal short-term generation scheduling for 10 generating units using particle swarm optimization (PSO). The scheduling problem is formulated to minimize operating costs while satisfying constraints like power balance, unit limits, minimum up/down times, and spinning reserve requirements. PSO is described as an evolutionary algorithm that finds the global best solution by updating particle velocities and positions based on the particle's own experience and the experience of neighboring particles. The steps of applying PSO to the scheduling problem are outlined, with particles initialized randomly within unit limits and then updated iteratively until an optimal schedule is found.
IRJET- Optimal Generation Scheduling for Thermal UnitsIRJET Journal
ย
This document summarizes a research paper that develops an optimal short-term generation scheduling model for 10 generating units using particle swarm optimization (PSO). The objective is to minimize total operating costs including fuel costs and start-up costs while satisfying constraints like power balance, generator limits, minimum up/down times, and reserve requirements. PSO is applied to obtain the optimal scheduling by updating the velocity and position of "particles" representing generator outputs over iterations. Results show PSO efficiently finds near-optimal solutions and provides economic benefits compared to other techniques for solving short-term generation scheduling problems.
In this work, we propose to apply trust region optimization to deep reinforcement
learning using a recently proposed Kronecker-factored approximation to
the curvature. We extend the framework of natural policy gradient and propose
to optimize both the actor and the critic using Kronecker-factored approximate
curvature (K-FAC) with trust region; hence we call our method Actor Critic using
Kronecker-Factored Trust Region (ACKTR). To the best of our knowledge, this
is the first scalable trust region natural gradient method for actor-critic methods.
It is also a method that learns non-trivial tasks in continuous control as well as
discrete control policies directly from raw pixel inputs. We tested our approach
across discrete domains in Atari games as well as continuous domains in the MuJoCo
environment. With the proposed methods, we are able to achieve higher
rewards and a 2- to 3-fold improvement in sample efficiency on average, compared
to previous state-of-the-art on-policy actor-critic methods. Code is available at
https://github.com/openai/baselines.
The document discusses the QTPIE model for modeling electrostatics in water. It summarizes the key aspects of the QTPIE model, including defining charge-transfer variables and attenuated electronegativity to model polarization. It also discusses challenges in numerically solving the QTPIE equations and compares calculated dipole moments and polarizabilities to ab initio results. The QTPIE model is able to reproduce ab initio dipole moments but underestimates polarizabilities due to a potential error in the polarizability formula.
27.docking protein-protein and protein-ligandAbhijeet Kadam
ย
This document discusses protein-protein and protein-ligand docking. It begins by defining docking as determining whether two biological molecules interact and finding their lowest energy orientation if so. The document then discusses challenges like the large number of possible conformations and small energy changes. It describes different docking study types and techniques used, including surface representation methods and algorithms like DOCK and RosettaDOCK. Finally, it summarizes a protein-protein docking algorithm and notes current problems in docking relate to limited flexibility handling and scoring function efficiency.
Molecular docking involves determining the optimal orientation of two biological molecules to maximize their interaction and minimize their total energy. It is important for understanding protein-protein interactions and rational drug design. Docking programs represent molecule surfaces and match them to find orientations, evaluating via scoring functions like shape complementarity, empirical potentials, or knowledge-based potentials derived from protein structures. Common techniques include representing surfaces as spheres or alpha shapes, and optimization methods like Monte Carlo, molecular dynamics, or genetic algorithms to introduce flexibility.
Advanced SOM & K Mean Method for Load Curve Clustering IJECEIAES
ย
From the load curve classification for one customer, the main features such as the seasonal factors, the weekday factors influencing on the electricity consumption may be extracted. By this way some utilities can make decision on the tariff by seasons or by day in week. The popular clustering techniques are the SOM & K-mean or Fuzzy K-mean. SOM &Kmean is a prominent approach for clustering with a two-level approach: first, the data set will be clustered using the SOM and in the second level, the SOM will be clustered by K-mean. In the first level, two training algorithms were examined: sequential and batch training. For the second level, the K-mean has the results that are strongly depended on the initial values of the centers. To overcome this, this paper used the subtractive clustering approach proposed by Chiu in 1994 to determine the centers. Because the effective radius in Chiuโs method has some influence on the number of centers, the paper applied the PSO technique to find the optimum radius. To valid the proposed approach, the test on well-known data samples is carried out. The applications for daily load curves of one Southern utility are presented.
Nucleon electromagnetic form factors at high-momentum transfer from Lattice QCDChristos Kallidonis
ย
This document summarizes a presentation on calculating the nucleon electromagnetic form factors at high momentum transfer using lattice QCD. Key points:
1) Lattice QCD simulations were performed on two ensembles with different volumes but similar lattice spacing to calculate the nucleon form factors up to momentum transfers of 12 GeV^2.
2) Boosted nucleon states were used in the simulations to access higher momentum transfers while keeping nucleon energies low. Three-point correlation functions were calculated to extract the matrix elements.
3) Plateaus in the ratio of three-point to two-point functions were identified to obtain the form factors, and two-state fits were also used to account for excited state contributions.
Optimal control of electrodynamic tether orbit transfersFrancisco Carvalho
ย
This document describes a new numerical technique for calculating optimal trajectories for dynamical systems with multiple timescales. The technique combines quadrature and pseudospectral methods using Chebyshev-Gauss-Lobatto points, which allows different meshes to be used for the fast and slow dynamics. This reduces the problem size compared to solving the full-scale problem. The method is applied to optimal control of electrodynamic tether orbit transfers, where the current varies fast compared to changes in orbital elements. Numerical results show the technique achieves high accuracy and spinning tethers can be more efficient for orbital maneuvering than hanging tethers.
Automated Generation of High-accuracy Interatomic Potentials Using Quantum Dataaimsnist
ย
Sandia National Laboratories is developing SNAP (Spectral Neighbor Analysis Potential) potentials for molecular dynamics simulations. SNAP potentials are fitted to quantum mechanical data using bispectrum components that describe the local atomic environments. SNAP potentials have been shown to accurately reproduce properties of tantalum, including liquid structure and screw dislocation behavior not included in the training data. Work is ongoing to develop multi-element SNAP potentials, including for tungsten-beryllium alloys relevant to modeling plasma-surface interactions in nuclear fusion reactors.
This document provides an overview of phonons and lattice dynamics as well as tips for using the phonopy software package. It discusses the theory of phonons in crystals and the harmonic and quasi-harmonic approximations. It also outlines the workflow for using phonopy to calculate forces, construct the dynamical matrix, and post-process results to obtain phonon dispersions, densities of states, and thermal properties. Helpful tips are provided for optimizing VASP settings for force calculations and manipulating phonopy settings and output files.
Pattern recognition binoy k means clustering108kaushik
ย
This document discusses clustering and the k-means clustering algorithm. It defines clustering as grouping a set of data objects into clusters so that objects within the same cluster are similar to each other but dissimilar to objects in other clusters. The k-means algorithm is described as an iterative process that assigns each object to one of k predefined clusters based on the object's distance from the cluster's centroid, then recalculates the centroid, repeating until cluster assignments no longer change. A worked example demonstrates how k-means partitions 7 objects into 2 clusters over 3 iterations. The k-means algorithm is noted to be efficient but requires specifying k and can be impacted by outliers, noise, and non-convex cluster shapes.
The document proposes a new approach combining fuzzy logic and particle swarm optimization (PSO) to optimally place static VAR compensators (SVCs) in power systems. Fuzzy logic is used to determine optimal locations for SVCs based on objectives of reducing power losses and maintaining voltages. PSO is then used to iteratively optimize the ratings of SVCs placed at the optimal locations for different loading conditions. The approach is tested on IEEE 14-bus and 30-bus test systems. Results show improved voltage profiles and reduced power losses with optimally placed and rated SVCs.
Similar to CP2K: How to use the constrained DFT module (20)
hematic appreciation test is a psychological assessment tool used to measure an individual's appreciation and understanding of specific themes or topics. This test helps to evaluate an individual's ability to connect different ideas and concepts within a given theme, as well as their overall comprehension and interpretation skills. The results of the test can provide valuable insights into an individual's cognitive abilities, creativity, and critical thinking skills
The debris of the โlast major mergerโ is dynamically youngSรฉrgio Sacani
ย
The Milky Wayโs (MW) inner stellar halo contains an [Fe/H]-rich component with highly eccentric orbits, often referred to as the
โlast major merger.โ Hypotheses for the origin of this component include Gaia-Sausage/Enceladus (GSE), where the progenitor
collided with the MW proto-disc 8โ11 Gyr ago, and the Virgo Radial Merger (VRM), where the progenitor collided with the
MW disc within the last 3 Gyr. These two scenarios make different predictions about observable structure in local phase space,
because the morphology of debris depends on how long it has had to phase mix. The recently identified phase-space folds in Gaia
DR3 have positive caustic velocities, making them fundamentally different than the phase-mixed chevrons found in simulations
at late times. Roughly 20 per cent of the stars in the prograde local stellar halo are associated with the observed caustics. Based
on a simple phase-mixing model, the observed number of caustics are consistent with a merger that occurred 1โ2 Gyr ago.
We also compare the observed phase-space distribution to FIRE-2 Latte simulations of GSE-like mergers, using a quantitative
measurement of phase mixing (2D causticality). The observed local phase-space distribution best matches the simulated data
1โ2 Gyr after collision, and certainly not later than 3 Gyr. This is further evidence that the progenitor of the โlast major mergerโ
did not collide with the MW proto-disc at early times, as is thought for the GSE, but instead collided with the MW disc within
the last few Gyr, consistent with the body of work surrounding the VRM.
ESR spectroscopy in liquid food and beverages.pptxPRIYANKA PATEL
ย
With increasing population, people need to rely on packaged food stuffs. Packaging of food materials requires the preservation of food. There are various methods for the treatment of food to preserve them and irradiation treatment of food is one of them. It is the most common and the most harmless method for the food preservation as it does not alter the necessary micronutrients of food materials. Although irradiated food doesnโt cause any harm to the human health but still the quality assessment of food is required to provide consumers with necessary information about the food. ESR spectroscopy is the most sophisticated way to investigate the quality of the food and the free radicals induced during the processing of the food. ESR spin trapping technique is useful for the detection of highly unstable radicals in the food. The antioxidant capability of liquid food and beverages in mainly performed by spin trapping technique.
ESPP presentation to EU Waste Water Network, 4th June 2024 โEU policies driving nutrient removal and recycling
and the revised UWWTD (Urban Waste Water Treatment Directive)โ
The binding of cosmological structures by massless topological defectsSรฉrgio Sacani
ย
Assuming spherical symmetry and weak field, it is shown that if one solves the Poisson equation or the Einstein field
equations sourced by a topological defect, i.e. a singularity of a very specific form, the result is a localized gravitational
field capable of driving flat rotation (i.e. Keplerian circular orbits at a constant speed for all radii) of test masses on a thin
spherical shell without any underlying mass. Moreover, a large-scale structure which exploits this solution by assembling
concentrically a number of such topological defects can establish a flat stellar or galactic rotation curve, and can also deflect
light in the same manner as an equipotential (isothermal) sphere. Thus, the need for dark matter or modified gravity theory is
mitigated, at least in part.
The technology uses reclaimed COโ as the dyeing medium in a closed loop process. When pressurized, COโ becomes supercritical (SC-COโ). In this state COโ has a very high solvent power, allowing the dye to dissolve easily.
The ability to recreate computational results with minimal effort and actionable metrics provides a solid foundation for scientific research and software development. When people can replicate an analysis at the touch of a button using open-source software, open data, and methods to assess and compare proposals, it significantly eases verification of results, engagement with a diverse range of contributors, and progress. However, we have yet to fully achieve this; there are still many sociotechnical frictions.
Inspired by David Donoho's vision, this talk aims to revisit the three crucial pillars of frictionless reproducibility (data sharing, code sharing, and competitive challenges) with the perspective of deep software variability.
Our observation is that multiple layers โ hardware, operating systems, third-party libraries, software versions, input data, compile-time options, and parameters โ are subject to variability that exacerbates frictions but is also essential for achieving robust, generalizable results and fostering innovation. I will first review the literature, providing evidence of how the complex variability interactions across these layers affect qualitative and quantitative software properties, thereby complicating the reproduction and replication of scientific studies in various fields.
I will then present some software engineering and AI techniques that can support the strategic exploration of variability spaces. These include the use of abstractions and models (e.g., feature models), sampling strategies (e.g., uniform, random), cost-effective measurements (e.g., incremental build of software configurations), and dimensionality reduction methods (e.g., transfer learning, feature selection, software debloating).
I will finally argue that deep variability is both the problem and solution of frictionless reproducibility, calling the software science community to develop new methods and tools to manage variability and foster reproducibility in software systems.
Exposรฉ invitรฉ Journรฉes Nationales du GDR GPL 2024
Travis Hills' Endeavors in Minnesota: Fostering Environmental and Economic Pr...Travis Hills MN
ย
Travis Hills of Minnesota developed a method to convert waste into high-value dry fertilizer, significantly enriching soil quality. By providing farmers with a valuable resource derived from waste, Travis Hills helps enhance farm profitability while promoting environmental stewardship. Travis Hills' sustainable practices lead to cost savings and increased revenue for farmers by improving resource efficiency and reducing waste.
2. Contents
โข Introduction: what is CDFT and why use it?
โข Theoretical basis of CDFT in brief
โข CDFT implementation in CP2K
o Algorithmic framework
o Overview of features using examples
โข Summary
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2
4. Introduction
โข CDFT allows creation of charge and spin localized states
โข Why are such states needed?
12.1.2018
3
5. Introduction
โข CDFT allows creation of charge and spin localized states
โข Why are such states needed?
o Charge transfer phenomena
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3
6. Introduction
โข CDFT allows creation of charge and spin localized states
โข Why are such states needed?
o Charge transfer phenomena
o Electronic couplings (key role in charge transfer kinetics)
12.1.2018
3
7. Introduction
โข CDFT allows creation of charge and spin localized states
โข Why are such states needed?
o Charge transfer phenomena
o Electronic couplings (key role in charge transfer kinetics)
o Treating self-interaction error due to spurious electron delocalization
12.1.2018
3
8. Introduction
โข CDFT allows creation of charge and spin localized states
โข Why are such states needed?
o Charge transfer phenomena
o Electronic couplings (key role in charge transfer kinetics)
o Treating self-interaction error due to spurious electron delocalization
o Parametrizing model Hamiltonians (e.g. Heisenberg spin Hamiltonian)
12.1.2018
3
9. Introduction
โข CDFT allows creation of charge and spin localized states
โข Why are such states needed?
o Charge transfer phenomena
o Electronic couplings (key role in charge transfer kinetics)
o Treating self-interaction error due to spurious electron delocalization
o Parametrizing model Hamiltonians (e.g. Heisenberg spin Hamiltonian)
o And moreโฆ [1]
1. Kaduk, B.; Kowalczyk, T.; van Voorhis, T., Chem. Rev., 2012, 112, 321โ370.
12.1.2018
3
10. Introduction
โข CDFT allows creation of charge and spin localized states
โข Why are such states needed?
o Charge transfer phenomena
o Electronic couplings (key role in charge transfer kinetics)
o Treating self-interaction error due to spurious electron delocalization
o Parametrizing model Hamiltonians (e.g. Heisenberg spin Hamiltonian)
o And moreโฆ [1]
โข CDFT in CP2K [2] requires version 5.1 or newer
1. Kaduk, B.; Kowalczyk, T.; van Voorhis, T., Chem. Rev., 2012, 112, 321โ370.
2. Holmberg, N.; Laasonen, K., J. Chem. Theory Comput., 2017, 13, 587โ601. 12.1.2018
3
11. Generation of constrained states
โข Enforce density localization in atom-centered regions with constraint
potential(s) [3,4]
๐ธ๐ธCDFT ๐๐, ๐๐ = max
๐๐
min
๐๐
๐ธ๐ธKS ๐๐ + ๏ฟฝ
๐๐
๐๐๐๐ ๏ฟฝ
๐๐=โ,โ
๏ฟฝ ๐ค๐ค๐๐
๐๐
๐๐ ๐๐๐๐
๐๐ ๐๐๐๐ โ ๐๐๐๐
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4
3. Wu, Q.; van Voorhis, T., Phys. Rev. A: At., Mol., Opt. Phys., 2005, 72, 024502.
4. Wu, Q.; van Voorhis, T., J. Chem. Theory Comput., 2006, 2, 765โ774.
12. Generation of constrained states
โข Enforce density localization in atom-centered regions with constraint
potential(s) [3,4]
๐ธ๐ธCDFT ๐๐, ๐๐ = max
๐๐
min
๐๐
๐ธ๐ธKS ๐๐ + ๏ฟฝ
๐๐
๐๐๐๐ ๏ฟฝ
๐๐=โ,โ
๏ฟฝ ๐ค๐ค๐๐
๐๐
๐๐ ๐๐๐๐
๐๐ ๐๐๐๐ โ ๐๐๐๐
10.1.2018
4
Weight
function
Lagrange multiplier (potential strength)
Target
value
3. Wu, Q.; van Voorhis, T., Phys. Rev. A: At., Mol., Opt. Phys., 2005, 72, 024502.
4. Wu, Q.; van Voorhis, T., J. Chem. Theory Comput., 2006, 2, 765โ774.
13. Generation of constrained states
โข Enforce density localization in atom-centered regions with constraint
potential(s) [3,4]
๐ธ๐ธCDFT ๐๐, ๐๐ = max
๐๐
min
๐๐
๐ธ๐ธKS ๐๐ + ๏ฟฝ
๐๐
๐๐๐๐ ๏ฟฝ
๐๐=โ,โ
๏ฟฝ ๐ค๐ค๐๐
๐๐
๐๐ ๐๐๐๐
๐๐ ๐๐๐๐ โ ๐๐๐๐
โข Weight function defines the type of constraint
10.1.2018
4
Weight
function
Lagrange multiplier (potential strength)
Target
value
3. Wu, Q.; van Voorhis, T., Phys. Rev. A: At., Mol., Opt. Phys., 2005, 72, 024502.
4. Wu, Q.; van Voorhis, T., J. Chem. Theory Comput., 2006, 2, 765โ774.
14. Generation of constrained states
โข Enforce density localization in atom-centered regions with constraint
potential(s) [3,4]
๐ธ๐ธCDFT ๐๐, ๐๐ = max
๐๐
min
๐๐
๐ธ๐ธKS ๐๐ + ๏ฟฝ
๐๐
๐๐๐๐ ๏ฟฝ
๐๐=โ,โ
๏ฟฝ ๐ค๐ค๐๐
๐๐
๐๐ ๐๐๐๐
๐๐ ๐๐๐๐ โ ๐๐๐๐
โข Weight function defines the type of constraint
o Total density constraint (๐๐โ
+ ๐๐โ
): ๐ค๐คโ
= ๐ค๐คโ
= ๐ค๐ค
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4
Weight
function
Lagrange multiplier (potential strength)
Target
value
3. Wu, Q.; van Voorhis, T., Phys. Rev. A: At., Mol., Opt. Phys., 2005, 72, 024502.
4. Wu, Q.; van Voorhis, T., J. Chem. Theory Comput., 2006, 2, 765โ774.
15. Generation of constrained states
โข Enforce density localization in atom-centered regions with constraint
potential(s) [3,4]
๐ธ๐ธCDFT ๐๐, ๐๐ = max
๐๐
min
๐๐
๐ธ๐ธKS ๐๐ + ๏ฟฝ
๐๐
๐๐๐๐ ๏ฟฝ
๐๐=โ,โ
๏ฟฝ ๐ค๐ค๐๐
๐๐
๐๐ ๐๐๐๐
๐๐ ๐๐๐๐ โ ๐๐๐๐
โข Weight function defines the type of constraint
o Total density constraint (๐๐โ
+ ๐๐โ
): ๐ค๐คโ
= ๐ค๐คโ
= ๐ค๐ค
o Magnetization density constraint (๐๐โ
โ ๐๐โ
): ๐ค๐คโ
= โ๐ค๐คโ
= ๐ค๐ค
10.1.2018
4
Weight
function
Lagrange multiplier (potential strength)
Target
value
3. Wu, Q.; van Voorhis, T., Phys. Rev. A: At., Mol., Opt. Phys., 2005, 72, 024502.
4. Wu, Q.; van Voorhis, T., J. Chem. Theory Comput., 2006, 2, 765โ774.
16. Generation of constrained states
โข Enforce density localization in atom-centered regions with constraint
potential(s) [3,4]
๐ธ๐ธCDFT ๐๐, ๐๐ = max
๐๐
min
๐๐
๐ธ๐ธKS ๐๐ + ๏ฟฝ
๐๐
๐๐๐๐ ๏ฟฝ
๐๐=โ,โ
๏ฟฝ ๐ค๐ค๐๐
๐๐
๐๐ ๐๐๐๐
๐๐ ๐๐๐๐ โ ๐๐๐๐
โข Weight function defines the type of constraint
o Total density constraint (๐๐โ
+ ๐๐โ
): ๐ค๐คโ
= ๐ค๐คโ
= ๐ค๐ค
o Magnetization density constraint (๐๐โ
โ ๐๐โ
): ๐ค๐คโ
= โ๐ค๐คโ
= ๐ค๐ค
o Spin specific constraint (๐๐โ): ๐ค๐คโ = ๐ค๐ค, ๐ค๐คโ = 0
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4
Weight
function
Lagrange multiplier (potential strength)
Target
value
3. Wu, Q.; van Voorhis, T., Phys. Rev. A: At., Mol., Opt. Phys., 2005, 72, 024502.
4. Wu, Q.; van Voorhis, T., J. Chem. Theory Comput., 2006, 2, 765โ774.
17. CDFT weight function
โข Constructed as sum of normalized
atomic weight functions
๐ค๐ค๐๐
๐๐
๐๐ = ๏ฟฝ๏ฟฝ
๐๐โ๐๐
๐๐๐๐ ๐๐๐๐(๐๐) ๏ฟฝ
๐๐
๐๐
๐๐๐๐(๐๐)
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18. CDFT weight function
โข Constructed as sum of normalized
atomic weight functions
๐ค๐ค๐๐
๐๐
๐๐ = ๏ฟฝ๏ฟฝ
๐๐โ๐๐
๐๐๐๐ ๐๐๐๐(๐๐) ๏ฟฝ
๐๐
๐๐
๐๐๐๐(๐๐)
โข CP2K uses Becke partitioning
o Smoothed Voronoi-like scheme
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19. CDFT weight function
โข Constructed as sum of normalized
atomic weight functions
๐ค๐ค๐๐
๐๐
๐๐ = ๏ฟฝ๏ฟฝ
๐๐โ๐๐
๐๐๐๐ ๐๐๐๐(๐๐) ๏ฟฝ
๐๐
๐๐
๐๐๐๐(๐๐)
โข CP2K uses Becke partitioning
o Smoothed Voronoi-like scheme
o Atomic sizes can be taken into account
(recommended)
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5
20. CDFT weight function
โข Constructed as sum of normalized
atomic weight functions
๐ค๐ค๐๐
๐๐
๐๐ = ๏ฟฝ๏ฟฝ
๐๐โ๐๐
๐๐๐๐ ๐๐๐๐(๐๐) ๏ฟฝ
๐๐
๐๐
๐๐๐๐(๐๐)
โข CP2K uses Becke partitioning
o Smoothed Voronoi-like scheme
o Atomic sizes can be taken into account
(recommended)
โ E.g. oxygen has positive charge in water
without adjustment
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21. Optimization of the CDFT energy (1/2)
โข Constraints are satisfied when
๐๐ ๐๐ =
๏ฟฝ
๐๐=โ,โ
๏ฟฝ ๐ค๐ค1
๐๐
๐๐ ๐๐๐๐
๐๐ ๐๐๐๐ โ ๐๐1
โฎ
= ๐๐
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22. Optimization of the CDFT energy (1/2)
โข Constraints are satisfied when
๐๐ ๐๐ =
๏ฟฝ
๐๐=โ,โ
๏ฟฝ ๐ค๐ค1
๐๐
๐๐ ๐๐๐๐
๐๐ ๐๐๐๐ โ ๐๐1
โฎ
= ๐๐
โข In practice, ๐๐ iteratively optimized until ๐ฆ๐ฆ๐๐๐๐ ๐๐ ๐๐ โค ๐๐
10.1.2018
6
23. Optimization of the CDFT energy (1/2)
โข Constraints are satisfied when
๐๐ ๐๐ =
๏ฟฝ
๐๐=โ,โ
๏ฟฝ ๐ค๐ค1
๐๐
๐๐ ๐๐๐๐
๐๐ ๐๐๐๐ โ ๐๐1
โฎ
= ๐๐
โข In practice, ๐๐ iteratively optimized until ๐ฆ๐ฆ๐๐๐๐ ๐๐ ๐๐ โค ๐๐
o Uses root-finding algorithms, e.g., Newtonโs method
๐๐๐๐+1 = ๐๐๐๐ โ ๐ผ๐ผ๐ฑ๐ฑ๐๐
โ1
๐๐ ๐๐๐๐
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24. Optimization of the CDFT energy (1/2)
โข Constraints are satisfied when
๐๐ ๐๐ =
๏ฟฝ
๐๐=โ,โ
๏ฟฝ ๐ค๐ค1
๐๐
๐๐ ๐๐๐๐
๐๐ ๐๐๐๐ โ ๐๐1
โฎ
= ๐๐
โข In practice, ๐๐ iteratively optimized until ๐ฆ๐ฆ๐๐๐๐ ๐๐ ๐๐ โค ๐๐
o Uses root-finding algorithms, e.g., Newtonโs method
๐๐๐๐+1 = ๐๐๐๐ โ ๐ผ๐ผ๐ฑ๐ฑ๐๐
โ1
๐๐ ๐๐๐๐
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Jacobian matrix,
approximated by
finite differences
Step size โ [โ1, 0)
๐ฑ๐ฑ๐๐๐๐ =
๐๐๐๐๐๐
๐๐๐๐๐๐
โ
๐๐๐๐ ๐๐ + ๐น๐น๐๐ โ ๐๐๐๐(๐๐)
๐น๐น๐๐
25. Optimization of the CDFT energy (2/2)
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7
Input
Constraints
converged
or max steps
reached?
Yes
New guess
for ๐๐
Output
CDFT loop
Store data for
mixed CDFT
Build Jacobian
(optional)
Optimize step
size?
Standard
CP2K SCF
Reduce
step size
No/Done
Yes
Yes
No
26. Defining constraints (1/2)
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7
&QS
...
&CDFT
TYPE_OF_CONSTRAINT BECKE
&OUTER_SCF ON
TYPE BECKE_CONSTRAINT
EXTRAPOLATION_ORDER 2
MAX_SCF 10
! Convergence threshold
EPS_SCF 1.0E-3
! Optimizer selection: now Newton's method with backtracking line search
OPTIMIZER NEWTON_LS
! Optimizer step size
STEP_SIZE -1.0
! Line search settings
MAX_LS 5
CONTINUE_LS
FACTOR_LS 0.5
! Finite difference settings for calculation of Jacobian matrix
JACOBIAN_STEP 1.0E-2
JACOBIAN_FREQ 1 1
JACOBIAN_TYPE FD1
JACOBIAN_RESTART FALSE
&END OUTER_SCF
&END CDFT Full example files at https://www.cp2k.org/howto:cdft
27. Defining constraints (2/2)
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8
&QS ! Constraint definitions
... ! Each repetition defines a constraint
&CDFT &ATOM_GROUP
... ATOMS 1
&END CDFT COEFF 1
&BECKE_CONSTRAINT CONSTRAINT_TYPE CHARGE
! Take atomic radii into account? &END ATOM_GROUP
ADJUST_SIZE FALSE ! No constraint but calculate charges
ATOMIC_RADII 0.63 0.32 &DUMMY_ATOMS
! Compute Becke charges? ATOMS 2
ATOMIC_CHARGES TRUE &END DUMMY_ATOMS
! Constraint strength and target values ! Print info about CDFT calculation
! Give one value per constraint &PROGRAM_RUN_INFO ON
STRENGTH ${BECKE_STR} &EACH
TARGET ${BECKE_TARGET} QS_SCF 1
! Cutoff scheme &END EACH
CUTOFF_TYPE ELEMENT COMMON_ITERATION_LEVELS 2
ELEMENT_CUTOFF 7.0 ADD_LAST NUMERIC
! Perform Becke partitioning only within the space FILENAME ./${NAME}
! spanned by constraint atom centered spherical Gaussians &END PROGRAM_RUN_INFO
! (reduces cost for solvated systems) &END BECKE_CONSTRAINT
CAVITY_CONFINE TRUE &END QS
CAVITY_SHAPE VDW
EPS_CAVITY 1.0E-7
IN_MEMORY TRUE
SHOULD_SKIP TRUE
28. Defining constraints (2/2)
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8
&QS ! Constraint definitions
... ! Each repetition defines a constraint
&CDFT &ATOM_GROUP
... ATOMS 1
&END CDFT COEFF 1
&BECKE_CONSTRAINT CONSTRAINT_TYPE CHARGE
! Take atomic radii into account? &END ATOM_GROUP
ADJUST_SIZE FALSE ! No constraint but calculate charges
ATOMIC_RADII 0.63 0.32 &DUMMY_ATOMS
! Compute Becke charges? ATOMS 2
ATOMIC_CHARGES TRUE &END DUMMY_ATOMS
! Constraint strength and target values ! Print info about CDFT calculation
! Give one value per constraint &PROGRAM_RUN_INFO ON
STRENGTH ${BECKE_STR} &EACH
TARGET ${BECKE_TARGET} QS_SCF 1
! Cutoff scheme &END EACH
CUTOFF_TYPE ELEMENT COMMON_ITERATION_LEVELS 2
ELEMENT_CUTOFF 7.0 ADD_LAST NUMERIC
! Perform Becke partitioning only within the space FILENAME ./${NAME}
! spanned by constraint atom centered spherical Gaussians &END PROGRAM_RUN_INFO
! (reduces cost for solvated systems) &END BECKE_CONSTRAINT
CAVITY_CONFINE TRUE &END QS
CAVITY_SHAPE VDW
EPS_CAVITY 1.0E-7
IN_MEMORY TRUE
SHOULD_SKIP TRUE
Use e.g. covalent radii
29. Defining constraints (2/2)
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&QS ! Constraint definitions
... ! Each repetition defines a constraint
&CDFT &ATOM_GROUP
... ATOMS 1
&END CDFT COEFF 1
&BECKE_CONSTRAINT CONSTRAINT_TYPE CHARGE
! Take atomic radii into account? &END ATOM_GROUP
ADJUST_SIZE FALSE ! No constraint but calculate charges
ATOMIC_RADII 0.63 0.32 &DUMMY_ATOMS
! Compute Becke charges? ATOMS 2
ATOMIC_CHARGES TRUE &END DUMMY_ATOMS
! Constraint strength and target values ! Print info about CDFT calculation
! Give one value per constraint &PROGRAM_RUN_INFO ON
STRENGTH ${BECKE_STR} &EACH
TARGET ${BECKE_TARGET} QS_SCF 1
! Cutoff scheme &END EACH
CUTOFF_TYPE ELEMENT COMMON_ITERATION_LEVELS 2
ELEMENT_CUTOFF 7.0 ADD_LAST NUMERIC
! Perform Becke partitioning only within the space FILENAME ./${NAME}
! spanned by constraint atom centered spherical Gaussians &END PROGRAM_RUN_INFO
! (reduces cost for solvated systems) &END BECKE_CONSTRAINT
CAVITY_CONFINE TRUE &END QS
CAVITY_SHAPE VDW
EPS_CAVITY 1.0E-7
IN_MEMORY TRUE
SHOULD_SKIP TRUE
Use e.g. covalent radii
31. Example: ๐๐๐ง๐ง๐๐
+
(1/2)
โข When ๐น๐น๐๐๐๐โ๐๐๐๐ grows, charge should localize onto one Zn atom
โข Standard GGA/hybrid functionals place +0.5 charge on both atoms
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32. Example: ๐๐๐ง๐ง๐๐
+
(1/2)
โข When ๐น๐น๐๐๐๐โ๐๐๐๐ grows, charge should localize onto one Zn atom
โข Standard GGA/hybrid functionals place +0.5 charge on both atoms
โข Force charge localization on first atom
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! Set initial constraint strength to 0 (restarting from DFT)
STRENGTH 0.0
! Constraint target is the number of valence electrons โ 1
TARGET 11.0
&ATOM_GROUP
ATOMS 1
COEFF 1
CONSTRAINT_TYPE CHARGE
&END ATOM_GROUP
33. Example: ๐๐๐ง๐ง๐๐
+
(2/2)
โข The default output file contains the CDFT SCF iterations
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New guess
for ๐๐
CDFT loop
Build Jacobian
(optional)
Optimize step
size?
Standard
CP2K SCF
Reduce
step size
No/Done
Yes
34. Example: ๐๐๐ง๐ง๐๐
+
(2/2)
โข The default output file contains the CDFT SCF iterations
o Each iteration corresponds to standard CP2K energy optimization
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New guess
for ๐๐
CDFT loop
Build Jacobian
(optional)
Optimize step
size?
Standard
CP2K SCF
Reduce
step size
No/Done
Yes
35. Example: ๐๐๐ง๐ง๐๐
+
(2/2)
โข The default output file contains the CDFT SCF iterations
o Each iteration corresponds to standard CP2K energy optimization
o Uses optimized solution from line search as restart if available
โข The following files are created with (quasi-)Newton optimizers
o *.LineSearch.out: Electronic structure SCF and optimization of step size
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10
New guess
for ๐๐
CDFT loop
Build Jacobian
(optional)
Optimize step
size?
Standard
CP2K SCF
Reduce
step size
No/Done
Yes
36. Example: ๐๐๐ง๐ง๐๐
+
(2/2)
โข The default output file contains the CDFT SCF iterations
o Each iteration corresponds to standard CP2K energy optimization
o Uses optimized solution from line search as restart if available
โข The following files are created with (quasi-)Newton optimizers
o *.LineSearch.out: Electronic structure SCF and optimization of step size
o *.cdftLog: Summary of CDFT parameters and computed partial charges
10.1.2018
10
37. Example: ๐๐๐ง๐ง๐๐
+
(2/2)
โข The default output file contains the CDFT SCF iterations
o Each iteration corresponds to standard CP2K energy optimization
o Uses optimized solution from line search as restart if available
โข The following files are created with (quasi-)Newton optimizers
o *.LineSearch.out: Electronic structure SCF and optimization of step size
o *.cdftLog: Summary of CDFT parameters and computed partial charges
o *.JacobianInfo.out: Calculation of Jacobian matrix with perturbed ๐๐
10.1.2018
10
38. Example: ๐๐๐ง๐ง๐๐
+
(2/2)
โข The default output file contains the CDFT SCF iterations
o Each iteration corresponds to standard CP2K energy optimization
o Uses optimized solution from line search as restart if available
โข The following files are created with (quasi-)Newton optimizers
o *.LineSearch.out: Electronic structure SCF and optimization of step size
o *.cdftLog: Summary of CDFT parameters and computed partial charges
o *.JacobianInfo.out: Calculation of Jacobian matrix with perturbed ๐๐
o *.inverseJacobian: Restart file for inverse Jacobian matrix
10.1.2018
10
39. Standard CP2K SCF with
fixed values of constraint
strength and step size
CDFT SCF iteration
information
Constraint
information
Restarted from converged
density obtained during
line search
41. Fragment constraints (1/2)
โข Number of valence electrons per
molecule not necessarily well
defined
o Case for overlapping, strongly
interacting molecules
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12
42. Fragment constraints (1/2)
โข Number of valence electrons per
molecule not necessarily well
defined
o Case for overlapping, strongly
interacting molecules
o How to set constraint target value?
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12
43. Fragment constraints (1/2)
โข Number of valence electrons per
molecule not necessarily well
defined
o Case for overlapping, strongly
interacting molecules
o How to set constraint target value?
โข Use a fragment based constraint
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๏ฟฝ๐๐A(๐๐) ๏ฟฝ๐๐B(๐๐)
๏ฟฝ๐๐๐๐ = ๏ฟฝ
๐๐=โ,โ
๏ฟฝ๐ค๐ค๐๐
๐๐ ๏ฟฝ๐๐A
๐๐
๐๐ + ๏ฟฝ๐๐B
๐๐
๐๐ ๐๐๐๐
44. Fragment constraints (1/2)
โข Number of valence electrons per
molecule not necessarily well
defined
o Case for overlapping, strongly
interacting molecules
o How to set constraint target value?
โข Use a fragment based constraint
o Only single-point calculations
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๏ฟฝ๐๐A(๐๐) ๏ฟฝ๐๐B(๐๐)
๏ฟฝ๐๐๐๐ = ๏ฟฝ
๐๐=โ,โ
๏ฟฝ๐ค๐ค๐๐
๐๐ ๏ฟฝ๐๐A
๐๐
๐๐ + ๏ฟฝ๐๐B
๐๐
๐๐ ๐๐๐๐
45. Fragment constraints (1/2)
โข Number of valence electrons per
molecule not necessarily well
defined
o Case for overlapping, strongly
interacting molecules
o How to set constraint target value?
โข Use a fragment based constraint
o Only single-point calculations
โข Cube read/write accelerated with
MPI I/O since r18131
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๏ฟฝ๐๐A(๐๐) ๏ฟฝ๐๐B(๐๐)
๏ฟฝ๐๐๐๐ = ๏ฟฝ
๐๐=โ,โ
๏ฟฝ๐ค๐ค๐๐
๐๐ ๏ฟฝ๐๐A
๐๐
๐๐ + ๏ฟฝ๐๐B
๐๐
๐๐ ๐๐๐๐
46. Fragment constraints (2/2)
โข Charge transfer energies of
strongly interacting complexes
โฮ๐ธ๐ธCT = ๐ธ๐ธCDFT โ ๐ธ๐ธDFT
10.1.2018
13
47. Fragment constraints (2/2)
โข Charge transfer energies of
strongly interacting complexes
โฮ๐ธ๐ธCT = ๐ธ๐ธCDFT โ ๐ธ๐ธDFT
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Energy of system with
charge transfer prevented
48. Fragment constraints (2/2)
โข Charge transfer energies of
strongly interacting complexes
โฮ๐ธ๐ธCT = ๐ธ๐ธCDFT โ ๐ธ๐ธDFT
10.1.2018
13
Energy of system with
charge transfer prevented
Fragment Becke with atomic size adjustments
Becke
Becke with atomic size adjustments
BW:
BW+A:
FBB+A:
49. Fragment constraints (2/2)
โข Charge transfer energies of
strongly interacting complexes
โฮ๐ธ๐ธCT = ๐ธ๐ธCDFT โ ๐ธ๐ธDFT
โข Magnitude of charge transferred,
ฮ๐๐ , overestimated by non-
fragment constraints
10.1.2018
13
Energy of system with
charge transfer prevented
Fragment Becke with atomic size adjustments
Becke
Becke with atomic size adjustments
BW:
BW+A:
FBB+A:
50. Combining multiple CDFT states
โข Additional properties can be computed from the interactions between
CDFT states
10.1.2018
14
51. Combining multiple CDFT states
โข Additional properties can be computed from the interactions between
CDFT states
o Charge transfer kinetics (Marcus theory)
๐๐ab =
2๐๐
โ
๐ฏ๐ฏab
2
๐๐
4๐๐๐๐๐๐๐๐
exp โ
๐๐ + ฮ๐ด๐ด 2
4๐๐๐๐๐๐๐๐
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14
52. Combining multiple CDFT states
โข Additional properties can be computed from the interactions between
CDFT states
o Charge transfer kinetics (Marcus theory)
๐๐ab =
2๐๐
โ
๐ฏ๐ฏab
2
๐๐
4๐๐๐๐๐๐๐๐
exp โ
๐๐ + ฮ๐ด๐ด 2
4๐๐๐๐๐๐๐๐
10.1.2018
14
Electronic coupling
Solvent reorganization energy
Reaction free energy
53. Combining multiple CDFT states
โข Additional properties can be computed from the interactions between
CDFT states
o Charge transfer kinetics (Marcus theory)
๐๐ab =
2๐๐
โ
๐ฏ๐ฏab
2
๐๐
4๐๐๐๐๐๐๐๐
exp โ
๐๐ + ฮ๐ด๐ด 2
4๐๐๐๐๐๐๐๐
o Configuration interaction within the basis of CDFT states
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14
Electronic coupling
Solvent reorganization energy
Reaction free energy
54. Combining multiple CDFT states
โข Additional properties can be computed from the interactions between
CDFT states
o Charge transfer kinetics (Marcus theory)
๐๐ab =
2๐๐
โ
๐ฏ๐ฏab
2
๐๐
4๐๐๐๐๐๐๐๐
exp โ
๐๐ + ฮ๐ด๐ด 2
4๐๐๐๐๐๐๐๐
o Configuration interaction within the basis of CDFT states
โข Approximate electronic coupling with CDFT Kohn-Sham determinants
after orthogonalization [5]
๐ฏ๐ฏij โ ๐ฝ๐ฝCDFT
i ๏ฟฝ๐ป๐ปKS ๐ฝ๐ฝCDFT
j
=
๐ธ๐ธCDFT
i
+ ๐ธ๐ธCDFT
j
2
๐บ๐บ๐๐๐๐ โ ๏ฟฝ
๐๐
๐ฝ๐ฝCDFT
i ๐๐๐๐
i
๐ค๐ค๐๐
i
(๐๐) + ๐๐๐๐
j
๐ค๐ค๐๐
j
(๐๐)
2 ๐ฝ๐ฝCDFT
j
10.1.2018
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Electronic coupling
Solvent reorganization energy
Reaction free energy
5. Wu, Q.; van Voorhis, T., J. Chem. Phys., 2006, 125, 164105.
55. The mixed CDFT module&MULTIPLE_FORCE_EVALS # Zn+ Zn
FORCE_EVAL_ORDER 2 3 &FORCE_EVAL
MULTIPLE_SUBSYS FALSE @SET WFN_FILE ${WFN_FILE_1}
&END @SET RESTART ${RESTART_1}
&FORCE_EVAL @SET NAME ${PROJECT_NAME}-state1
METHOD MIXED @SET BECKE_TARGET ${BECKE_TARGET_1}
&MIXED @SET BECKE_STR ${BECKE_STR_1}
MIXING_TYPE MIXED_CDFT METHOD QS
NGROUPS 1 @include ${DFT_FILE}
&MIXED_CDFT &END FORCE_EVAL
! Calculate mixed CDFT properties every COUPLING step # Zn Zn+
COUPLING 1 &FORCE_EVAL
! Settings determining how forces are mixed @SET WFN_FILE ${WFN_FILE_2}
FORCE_STATES 1 2 @SET RESTART ${RESTART_2}
LAMBDA 1.0 @SET NAME ${PROJECT_NAME}-state2
! Orthogonalize CDFT states with Lowdin's method @SET BECKE_TARGET ${BECKE_TARGET_2}
LOWDIN TRUE @SET BECKE_STR ${BECKE_STR_2}
! Configuration interaction? METHOD QS
CI FALSE @include ${DFT_FILE}
&PRINT &END FORCE_EVAL
&PROGRAM_RUN_INFO ON
&END
&END PRINT
&END MIXED_CDFT
&END MIXED
@include subsys.inc
&END FORCE_EVAL
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Additional settings available and
explained in the manual
58. Electronic coupling in ๐๐๐ง๐ง๐๐
+
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16
Zn+
Zn ๏ฟฝ๐ป๐ป ZnZn+
Different
orthogonalization
algorithms
59. Electronic coupling in ๐๐๐ง๐ง๐๐
+
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17
Zn+
Zn ๏ฟฝ๐ป๐ป ZnZn+
Different
orthogonalization
algorithms
Agrees with 5.49 mHartree
estimate from more expensive
wavefunction based method
CASSCF/MRCI+Q
60. CDFT in solvated systems
โข Computational efficiency of
GPW/OT allows study of solvated
charge transfer processes at full
DFT level
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18
61. CDFT in solvated systems
โข Computational efficiency of
GPW/OT allows study of solvated
charge transfer processes at full
DFT level
โข Evaluating intramolecular charge
transfer kinetics in QTTFQโ
โข 258 water, 12 ps (0.5 fs timestep)
โข 48 s/timestep @ 384 MPI cores
(~120k core hours)
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18
62. List of CDFT capabilities in CP2K
โข GPW and GAPW (no fragment constraint)
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19
63. List of CDFT capabilities in CP2K
โข GPW and GAPW (no fragment constraint)
โข Full DFT or QM/MM
12.1.2018
19
64. List of CDFT capabilities in CP2K
โข GPW and GAPW (no fragment constraint)
โข Full DFT or QM/MM
โข Primarily for OT, diagonalization is supported but difficult to converge
12.1.2018
19
65. List of CDFT capabilities in CP2K
โข GPW and GAPW (no fragment constraint)
โข Full DFT or QM/MM
โข Primarily for OT, diagonalization is supported but difficult to converge
โข Energies and forces for an unlimited number of constraints (any type)
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19
66. List of CDFT capabilities in CP2K
โข GPW and GAPW (no fragment constraint)
โข Full DFT or QM/MM
โข Primarily for OT, diagonalization is supported but difficult to converge
โข Energies and forces for an unlimited number of constraints (any type)
โข Mixed CDFT module supports
12.1.2018
19
67. List of CDFT capabilities in CP2K
โข GPW and GAPW (no fragment constraint)
โข Full DFT or QM/MM
โข Primarily for OT, diagonalization is supported but difficult to converge
โข Energies and forces for an unlimited number of constraints (any type)
โข Mixed CDFT module supports
o Electronic couplings with various orthogonalization methods
12.1.2018
19
68. List of CDFT capabilities in CP2K
โข GPW and GAPW (no fragment constraint)
โข Full DFT or QM/MM
โข Primarily for OT, diagonalization is supported but difficult to converge
โข Energies and forces for an unlimited number of constraints (any type)
โข Mixed CDFT module supports
o Electronic couplings with various orthogonalization methods
o Configuration interaction
12.1.2018
19
69. List of CDFT capabilities in CP2K
โข GPW and GAPW (no fragment constraint)
โข Full DFT or QM/MM
โข Primarily for OT, diagonalization is supported but difficult to converge
โข Energies and forces for an unlimited number of constraints (any type)
โข Mixed CDFT module supports
o Electronic couplings with various orthogonalization methods
o Configuration interaction
o Removal of linearly-dependent MOs via SVD decomposition
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19
70. List of CDFT capabilities in CP2K
โข GPW and GAPW (no fragment constraint)
โข Full DFT or QM/MM
โข Primarily for OT, diagonalization is supported but difficult to converge
โข Energies and forces for an unlimited number of constraints (any type)
โข Mixed CDFT module supports
o Electronic couplings with various orthogonalization methods
o Configuration interaction
o Removal of linearly-dependent MOs via SVD decomposition
o Electronic coupling reliability metrics
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72. Summary
โข CDFT is a tool to study charge transfer phenomena
โข Available in latest release version
12.1.2018
20
73. Summary
โข CDFT is a tool to study charge transfer phenomena
โข Available in latest release version
โข Tutorial at https://www.cp2k.org/howto:cdft that complements regtests
12.1.2018
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74. Summary
โข CDFT is a tool to study charge transfer phenomena
โข Available in latest release version
โข Tutorial at https://www.cp2k.org/howto:cdft that complements regtests
o Summaries of CDFT theory and the CP2K implementation
o Walk throughs of example calculations
12.1.2018
20
75. Summary
โข CDFT is a tool to study charge transfer phenomena
โข Available in latest release version
โข Tutorial at https://www.cp2k.org/howto:cdft that complements regtests
o Summaries of CDFT theory and the CP2K implementation
o Walk throughs of example calculations
โข Help provided on Google groups if you encounter issues with CDFT
features
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