Add graphical abstract support

config.toml

@@ -8,7 +8,7 @@ theme = "beautifulhugo"
 #  homeTitle = ""
   subtitle = "QUantum Excited STates database"
 [[Params.bigimg]]
-  src = "img/montain.jpeg"
+  src = "data/publis/10/1021/acs/jctc/8b00406/picture.jpeg"
   desc = "A mountaineering analogy of the QUEST project"
 [markup]
   [markup.goldmark]

content/publications.html

@@ -26,7 +26,7 @@ draft: false
     const uospublis = spubliscite.format('data', { format: 'object' })
     const spublis = uospublis.sort((puba,pubb)=>pubUtils.getIssuedDate(puba) - pubUtils.getIssuedDate(pubb))
     for (const publi of spublis) {
-      art=createPubliUI(publi,pubs.sets,true)
+      art= await createPubliUI(publi,pubs.sets,true,true)
       $(art).appendTo("#publis_sets")
     }
     const odois=Array.from(pubs.others.keys())
@@ -34,7 +34,7 @@ draft: false
     const uoopublis = opubliscite.format('data', { format: 'object' })
     const opublis = uoopublis.sort((puba,pubb)=>pubUtils.getIssuedDate(puba) - pubUtils.getIssuedDate(pubb))
     for (const publi of opublis) {
-      art=createPubliUI(publi,pubs.others,true)
+      art= await createPubliUI(publi,pubs.others,true,true)
       $(art).appendTo("#publis_others")
     }
   }

static/css/publi.css

@@ -11,6 +11,12 @@
   padding: 0;
   border: 0
 }
+.publi .abstract > figure.picture{
+  width: 60%;
+  padding: 0px;
+  margin: 10px;
+  float: right;
+}
 
 .publi ul.authors-list li.author-item{
   display: inline;

static/data/publis/10/1021/acs/jctc/0c00227/abstract.html

@@ -0,0 +1 @@
+Aiming at completing the sets of FCI-quality transition energies that we recently developed (<i>J. Chem. Theory Comput.</i><b>2018</b>, <i>14</i>, 4360–4379, <i>ibid.</i><b>2019</b>, <i>15</i>, 1939–1956, and <i>ibid.</i><b>2020</b>, <i>16</i>, 1711–1741), we provide, in the present contribution, ultra-accurate vertical excitation energies for a series of “exotic” closed-shell molecules containing F, Cl, P, and Si atoms and small radicals, such as CON and its variants, that were not considered to date in such investigations. This represents a total of 81 high-quality transitions obtained with a series of diffuse-containing basis sets of various sizes. For the exotic compounds, these transitions are used to perform benchmarks with a vast array of lower level models, i.e., CIS(D), EOM-MP2, (SOS/SCS)-CC2, STEOM-CCSD, CCSD, CCSDR(3), CCSDT-3, (SOS-)ADC(2), and ADC(3). Additional comparisons are made with literature data. For the open-shell compounds, we  compared the performance of both the unrestricted and the restricted open-shell CCSD and CC3 formalisms.

static/data/publis/10/1021/acs/jctc/8b00406/abstract.html

@@ -0,0 +1 @@
+Striving to define very accurate vertical transition energies, we perform both high-level coupled cluster (CC) calculations (up to CCSDTQP) and selected configuration interaction (sCI) calculations (up to several millions of determinants) for 18 small compounds (water, hydrogen sulfide, ammonia, hydrogen chloride, dinitrogen, carbon monoxide, acetylene, ethylene, formaldehyde, methanimine, thioformaldehyde, acetaldehyde, cyclopropene, diazomethane, formamide, ketene, nitrosomethane, and the smallest streptocyanine). By systematically increasing the order of the CC expansion, the number of determinants in the CI expansion as well as the size of the one-electron basis set, we have been able to reach near full CI (FCI) quality transition energies. These calculations are carried out on CC3/<i>aug</i>-cc-pVTZ geometries, using a series of increasingly large atomic basis sets systematically including diffuse functions. In this way, we define a list of 110 transition energies for states of various characters (valence, Rydberg, n → π<sup>*</sup>, π → π*, singlet, triplet, etc.) to be used as references for further calculations. Benchmark transition energies are provided at the <i>aug</i>-cc-pVTZ level as well as with additional basis set corrections, in order to obtain results close to the complete basis set limit. These reference data are used to benchmark a series of 12 excited-state wave function methods accounting for double and triple contributions, namely ADC(2), ADC(3), CIS(D), CIS(D<sub>∞</sub>), CC2, STEOM-CCSD, CCSD, CCSDR(3), CCSDT-3, CC3, CCSDT., and CCSDTQ. It turns out that CCSDTQ yields a negligible difference with the extrapolated CI values with a mean absolute error as small as 0.01 eV, whereas the coupled cluster approaches including iterative triples are also very accurate (mean absolute error of 0.03 eV). Consequently, CCSDT-3 and CC3 can be used to define reliable benchmarks. This observation does not hold for ADC(3) that delivers quite large errors for this set of small compounds, with a clear tendency to overcorrect its second-order version, ADC(2). Finally, we discuss the possibility to use basis set extrapolation approaches so as to tackle more easily larger compounds.

static/data/publis/10/1021/acs/jctc/8b01205/abstract.html

@@ -0,0 +1 @@
+Excited states exhibiting double-excitation character are notoriously difficult to model using conventional single-reference methods, such as adiabatic time-dependent density functional theory (TD-DFT) or equation-of-motion coupled cluster (EOM-CC). In addition, these states are typical experimentally “dark”, making their detection in photoabsorption spectra very challenging. Nonetheless, they play a key role in the faithful description of many physical, chemical, and biological processes. In the present work, we provide accurate reference excitation energies for transitions involving a substantial amount of double excitation using a series of increasingly large diffuse-containing atomic basis sets. Our set gathers 20 vertical transitions from 14 small- and medium-size molecules (acrolein, benzene, beryllium atom, butadiene, carbon dimer and trimer, ethylene, formaldehyde, glyoxal, hexatriene, nitrosomethane, nitroxyl, pyrazine, and tetrazine). Depending on the size of the molecule, selected configuration interaction (sCI) and/or multiconfigurational (CASSCF, CASPT2, (X)MS-CASPT2, and NEVPT2) calculations are performed in order to obtain reliable estimates of the vertical transition energies. In addition, coupled cluster approaches including at least contributions from iterative triples (such as CC3, CCSDT, CCSDTQ, and CCSDTQP) are assessed. Our results clearly evidence that the error in CC methods is intimately related to the amount of double-excitation character of the transition. For “pure” double excitations (i.e., for transitions which do not mix with single excitations), the error in CC3 can easily reach 1 eV, while it goes down to a few tenths of an electronvolt for more common transitions (such as in <i>trans</i>-butadiene) involving a significant amount of singles. As expected, CC approaches including quadruples yield highly accurate results for any type of transition. The quality of the excitation energies obtained with multiconfigurational methods is harder to predict. We have found that the overall accuracy of these methods is highly dependent on both the system and the selected active space. The inclusion of the σ and σ* orbitals in the active space, even for transitions involving mostly π and π* orbitals, is mandatory in order to reach high accuracy. A theoretical best estimate (TBE) is reported for each transition. We believe that these reference data will be valuable for future methodological developments aiming at accurately describing double excitations.

static/data/publis/10/1021/acs/jctc/9b01216/abstract.html

@@ -0,0 +1 @@
+<p class="articleBody_abstractText">Following our previous work focusing on compounds containing up to 3 non-hydrogen atoms [<i>J. Chem. Theory Comput.</i><b>2018</b>, <i>14</i>, 4360–4379], we present here highly accurate vertical transition energies obtained for 27 molecules encompassing 4, 5, and 6 non-hydrogen atoms: acetone, acrolein, benzene, butadiene, cyanoacetylene, cyanoformaldehyde, cyanogen, cyclopentadiene, cyclopropenone, cyclopropenethione, diacetylene, furan, glyoxal, imidazole, isobutene, methylenecyclopropene, propynal, pyrazine, pyridazine, pyridine, pyrimidine, pyrrole, tetrazine, thioacetone, thiophene, thiopropynal, and triazine. To obtain these energies, we use equation-of-motion/linear-response coupled cluster theory up to the highest technically possible excitation order for these systems (CC3, EOM-CCSDT, and EOM-CCSDTQ) and selected configuration interaction (SCI) calculations (with tens of millions of determinants in the reference space), as well as the multiconfigurational <i>n</i>-electron valence state perturbation theory (NEVPT2) method. All these approaches are applied in combination with diffuse-containing atomic basis sets. For all transitions, we report at least CC3/<i>aug</i>-cc-pVQZ vertical excitation energies as well as CC3/<i>aug</i>-cc-pVTZ oscillator strengths for each dipole-allowed transition. We show that CC3 almost systematically delivers transition energies in agreement with higher-level methods with a typical deviation of ±0.04 eV, except for transitions with a dominant double excitation character where the error is much larger. The present contribution gathers a large, diverse, and accurate set of more than 200 highly accurate transition energies for states of various natures (valence, Rydberg, singlet, triplet, <i>n</i> → π*, π → π*, ...). We use this series of theoretical best estimates to benchmark a series of popular methods for excited state calculations: CIS(D), ADC(2), CC2, STEOM-CCSD, EOM-CCSD, CCSDR(3), CCSDT-3, CC3, and NEVPT2. The results of these benchmarks are compared to the available literature data.</p>

static/data/publis/10/1021/acs/jpclett/0c00014/abstract.html

@@ -0,0 +1 @@
+We provide an overview of the successive steps that made it possible to obtain increasingly accurate excitation energies with computational chemistry tools, eventually leading to chemically accurate vertical transition energies for small- and medium-size molecules. First, we describe the evolution of <i>ab initio</i> methods employed to define benchmark values, with the original Roos CASPT2 method, then the CC3 method as in the renowned Thiel set, and more recently the resurgence of selected configuration interaction methods. The latter method has been able to deliver consistently, for both single and double excitations, highly accurate excitation energies for small molecules, as well as medium-size molecules with compact basis sets. Second, we describe how these high-level methods and the creation of representative benchmark sets of excitation energies have allowed the fair and accurate assessment of the performance of computationally lighter methods. We conclude by discussing possible future theoretical and technological developments in the field.

static/js/createPubliUI.js

@@ -1,4 +1,8 @@
-function createPubliUI(publi,sets=new Map(),toolTips=false) {
+function getPubliSubDir(DOI) {
+  return DOI.split(".").join("/")
+}
+
+async function createPubliUI(publi,sets=new Map(),toolTips=false,abstract=false) {
   const art = $("<article/>").addClass("publi")
   art.className = "publi"
   if (sets.has(publi.DOI) && sets.get(publi.DOI)!==null) {
@@ -68,5 +72,16 @@ function createPubliUI(publi,sets=new Map(),toolTips=false) {
     month: "short",
     year: "numeric"
   }))).appendTo(art)
+  if (abstract) {
+   const dir = "/data/publis/"+getPubliSubDir(publi.DOI)
+   var ab = $("<section>",{id: "abstract",}).addClass("well").addClass("abstract")
+   var abfig =$("<figure>").addClass("picture")
+   abfig.appendTo(ab)
+   $("<img>",{src:dir+"/picture.jpeg"}).appendTo(abfig)
+   var htmltxt =await getTextFromFileUrlAsync(dir+"/abstract.html")
+   abtxt=$("<p>").html(htmltxt)
+   abtxt.appendTo(ab)
+   art.append(ab)
+  }
   return art
 }

static/js/getPublis.js

@@ -1,5 +1,5 @@
 async function getPublis() {
-  const text = await getTextFromFileUrlAsync("/data/publis.yaml")
+  const text = await getTextFromFileUrlAsync("/data/publis/index.yaml")
   const myYaml=jsyaml.load(text);
   myYaml.sets= ((myYaml.sets===null) ? new Map() : new Map(Object.entries(myYaml.sets)));
   myYaml.others=((myYaml.others===null) ? new Map() : new Map(Object.entries(myYaml.others)));