i were slightly sick today so couldnt do very well iteration on the happy day hackathon in work. but iterated also.

I discovered about how to use open md software, but I observe its not using quantum mechanics solution but rather using mechanistical interpretation of Leonnard-James definition and tackles it like a mechanical system with approximating the qm based bonds in the force field file. 

or I had not explored it yet and maybe it actually has also n body schrodinger equation solvers to generate calculate the moleculer interactions other than force fields which are experimental data as I guess or data taken from qm equation solvers/predictions.

yayyy but been wondering about these software and nice to get introduced. if i werent sick i mgiht iterated more. now i would continue with investigating another molecular simulator which is as good as openmd but also supporting the nbody schrodinger eq solution. to handle covalent bonds. or to be able to for instance apply some magnetic field and to be able to solve that quantum mechanics equation. since the factory is about binding creating covalent bonds or dispersion forces etc or the dipole moments and charge based forces and also some long distance forces in addition to short distance forces, so its about not using a statistical calculated force field of a polymer or molecule or atom etc but instead altering it to be able to try building covalent bonds ourselves. and i not surely knowing, but seems as that might be impossible wiht a static values based approach, cause the qm situation might completely change in a magnetic field i guess. so it needs to be solved dynamically.

for that schrodinger solver, i saw some software already exists like Gaussian like famous tool but its not open source.

and though hadnt investigated this that much but i believe it might be possible to write the solver ourselves somehow. and but of course need to study the solution options/methods provided used.

nice that we have force field files ready so we already know how it should behave i mean test data to test whether schrodinger eq solver is working correct or not is ready.

so i guess, what needs to be done in such product is: doing this generative design thing with varying the electromagnetic field or external forces inside a system to try to alter covalent bond structure or ionization structure with also that could be also altered. 

so that as a result, we could investigate how to bind the covalent bonds or how to break them efficiently or modify them. though energy required to do that is yet unknown by me. i mean i would see when qm solver is solving. 

this has been interesting to learn about, i hadnt finished LAMMPs toolkit reading any. cqause i moved to openmd first before that. and but would check Lammps now to see if it has if it includes quantum mechanics solvers thqat could be utilized.

cause this static solvers force fields based approach is good for simulators. but not good for building molecules from scratch or debonding or bonding etc. its good for moleculer simulations or matter phase any such simulations. 

i quite liked the software and its usage pattern surely. most i guess most data ocming from experimental physics that forcefield values of atoms/molecules etc.  (or could be calculated values for some i dont know, had not read fully yet).

hmm so recent goal came up to step of writing my own code instead of using openmd like tools unfortunately. since i need a qm simulator. 

should would i go to gauges level i mean sub atomic particles level to model those strong force interactions also? 

i have suhc particle physics book. but i am not sure on that. i guess their physics might be also quantum physics based maybe, i had not any studied sub atomic physics any nor particle physics any i mean.

 but the electron movements is surely modeled well by quantum physics and bonding behavior using the electron orbit. and the mehcanistical representations of it approximations of it through spring based systems with Leonard James i guess it were like that. 

so in one hand in openmd i saw mechanistical simulator and omission of qm calculators. but i might be wrong since i hadnt studied the simulator in detaul

and also lammps would be investigated more to get info if i has qm solvers if it has and if we could apply even magnetic field definitons ot the simujlator, it might be cool. but i dont know if it has such stuff.  maybe its also like openmd and mechanical (approximating qm side, or else it could be dynamically calculating either, i have no idea)

so i am very happy to have learnt about openmd. but due to being sick (since i couldnt had rested well yesterday) i hadnt iterated well since i am very sleepy due to lack of sleep and result of feeling sick due to that. 

it has been quite exciting to learn about at least one simulator and but still would continue to study. and would decide the path on how to implement this generative molecule design studio solution. i mean like how to design create process of fructose creation with just elements i mean atoms or molecules (that are not fructose :) ).   maybe we could also find a way to capture air's co2 co's carbon oxygen side using this methodology to find an efficient debonding method to reduce carbon footprint in air to some level. but it might not be existing such solution any. so it would be investigated some blind generative methods wise initially i guess with quantum physics solvers and alterations of magnetic fields. maybe with some magnetic field configuration and some external atoms it might be possible to debond carbon and collect carbon with plankton like devices but wind turbines based systems maybe or such systems.  but it might be impossible to do so either. its unknown yet by me since i am new to molecular engineering type topics. 

if we had some method to debond carbon atom (alike planktons or plants) it would had been awesome i guess to apply such solution. but its not know if such solution might exist or not. plus that pipes that air would pass that electromagnetic fonfigurations that which they would pass, how much air they would be able to process at one rotation it wouldnt be might not be a very efficient system. or could be. anyway. 

if we make a more efficient than planktons or plants type ssystems, we might save atmosphere from excess such carbon based content. and if at the same time if we could collect that taken from air carbon stuff to create fructose or cellulose lactose glucose, we might also at the same time generate food from that i mean food source food carbon source might come from air in that sense. 

btu all hypothethical. i mean if it were possible to do this, people might already had built it.

but its better to check if its possible or not. i mean to alter the bonding/debonding of such molecules and their intricate quantum system to debond them and even maybe using some nanobots in air to collect carbon atoms from air? with nanobots being moved flowed either through brownian movement or some field based movement. hmm i think maybe debonding c from o or o2 might be possible with nanobots that might be able to debond the c if its possible.

it might be possible. and if that nanobots would be let to flow to another end of a system in that air filtering system, the carbon content might be also collected via that. but how much air such system could process is unknown. at least such filter might help reduce environment pollution from factories etc i guess. 

hmm but as mentioned to investigate this bonding debonding/ buidling fructose from scratch like stuff or from air,  i need to build a n body schrodinger solver that could also take in to account the magnetic fields. and not only that i might need to go to subatomic particles level e.g. gauges world of particle physics. 

but for this i might need a very huge optimization skills or huge computing power unless i simplify maths of. simplifying maths of solvers is also some solved topic by someone that i would try to understand his workd (which reduces np to p) and would try to use that solver in the solution. and also i would investigate mathemathical groups that used in the solution of that diff. eqyation of matrices that might also have some chances to get optimized or with some methods to reduce compress functions maybe using number theory wise group knowledge and investigating such groups to see if such operations functions/mappings could be compressed represented in a compressed way.

ok i again made the topic to an overly complex engineering problem but its i think like that inherently already. there is nothing complexity i add myself, its inherently like that.

i wish it could be noncomplex that i could had used the preready simulators instead, but that be not possible. since they have some baseline static parameter configurations as force fields.

so again came up to the point of needing to write a quanrtum mechanicms simualtor code. 

but i also need to iterate in coder ai project in tandem. 

but i believe maybe its better to accompllish them in tandem, so that it becomes less boring when it feels boring when studying to same topics for long period, e.g. studying to phd topics in topoilogy autodidactively sometimes takes a lot time. 

i think i liked this idea of adding another such hobby project. of writing my own n body schrodinger eq solver to simulatoe the dynamics using the very ingenious approaches of approximations and investigating other possible solutions either also.

maybe before writing any qm simulaotr, i think i could use openmd to do soime reinforcement learning wise analysis without any additional external force field be present, so could follow mechanistical approach first. e.g. hey there might be still utility to investigate?but how i could do that without being able to simulate covalent bodning and dihedral angles formation itself.

lets continue reading documentation of this.

maybe it could with leonard jones potential logic, might do create also new covelant bonds? nope unless you specify in static field such possible configurations, its not working like that.

so might still need such tool. but in other wise, this tool could be investigated to build nanobots still.  of creating torsion based movement or chargd particles possible movements. so could be used with reinforcement learning like that. but for that we need to be able to deicpher whether such movement that is cyclic happens in some configurations. maybe with some quaternion based analysis. so cvhecking circularity in a change of configuration of n particles to check if cyclic movement happens  hmm that might be a nice study to create such group theoretic pattern matcher framework to understand if movement adheres to a patternt hat could be used as a nanobot mechanism. so in that sense, reinforcement learning and such pattern matcher might be run with spot instances on a public cloud to do iteratively investigate. but i dont think spot instances of cloud wouold be compatible with most mpi open mp based environments or could be. i dont know. i need to check. hmm this way we could just blind sight investigate the generative nanobot design methods, to see patterns in movement of molecules i mean knowledge ratio among the molecules movement specifically close molecules to see if some pattern happening and if its cyclic or not or a common non cyclic sequence like ocnstantly iterating change happens? unbounded sequence like? so we might need to have motion analyzers in this system to understand if the molecules adhere to any pattern that could be used as nanobots base units. but also debonding of suhc moleculer configuration should be power input wise high since it shouldnt be able to interact broke with the other external system like other molecules easialy. it should be not easy to disassociate such nanobto configuration i think. hmm so this simulator might had been used for such nanbot design crafting to then use them in fructose crafting. or glucose. 

hmm so i would check cheapest available cloud options to use for this investigation and would do some group theoretic checks on how to captures patterns of movement that could be repetitive and used asa nanobot patterns. so knowledge versus entropy topic, we want some knowledge from the configuration.  hmm so it could be even filtered with knowledge level. yupp. hmm so that but that knowledge patterns specific movement pattern might be captured with some group theoretic wise  pattern matcher to be devised. 

yayyy i liked this hobby project, becuase i were doing laziness to revising quantum mechanics knowledge right away or particle physics knowledge. that should be eventually studied. but i wanted to see some pragmatic results with some preready tools already available in such project in advance. since i been studying to theoretical topics in maths for a long time, i just wished some practical practice having project e.g. this openmd simulator for instance that i dont have to learn something to code a simulator but its already ready available.

cool. i liked this second project whihc would need lesser theoretical topics studying. 

only thing is devising the patten matcher of movement rotation patterns matcher part of the reinforcement learning based or just even simpler generative design approach it would be. so knowledge/entropy calculations is easy to do so imho. but should be thought on clearly surely and algorithm should be devised. but the pattern movement patgtern capturer would be interesting to design. needs groupt heoretic study there surely. ok this project is very practical. no theoretical background study that would take alot time to study is needed. just might revise ssome group theoretical topics and related to quaternions either or such other topics to devise it. so not like other projects that needed alot backgroun theoretical studies that still i study to (e.g. coder ai needs a lot theoretical topics studying etc)

i were very upset that i came again to the point of havinng have to write a quantuym mechanics smulator myself. that felt very upset/unhappy about it since it would meant again studying to theoretical topics/revising some and some hard work of such concepts regarding simulating atoms and even maybe subatomic. so much happy that i figured out an alternative path that i could use a tool instead of writing the tool myself whihc felt very overwhelming since it would had meant again a lot of effort. i were trying to intending to postpone coding of quantum mechanics simulator to delegate it to coder ai instead of me trying to code. so i were very unhappy when i discovered i need to write the quantum mechanis simulator again came to that point. but right now very happy that, i figured out an alternative porject type and is a practical project instead of needing lots of theoretical studies, but not much needing alot studies. i can even start coding it unlike coder ai project which i still do theoretical study for a very long time (maybe from 2021's beginning i think)  its very happy to find a project type that is this time very practical practices having type. i mean instead of endless theoretical studies i could just switch to implementation in this nanobot generative design project type, isnce i think this openmd simulator might be used directly. ah its so happy that i have a proejct that i dont have to write simulator of . were very unhappy some time today when i discovered i came to the same point of: i have to write a quantuym mechanics simulator myseklf. though that is not huge challenge actually. could be handled in a month. or more. but just i have other things to study to in tandem like coder ai project and its theoretical study. i mean quantum mechanics simulatoer would had been just atoms simulator. not something also like CAD or so software like physical itnerctions wont be present so it would be faster to have coded. but i definitely right now lack energy to spare to another theoretical studying needing project. i am full of theoretical studying tasks in my other project whihc is coder ai project.  

i am rihgt away so much happy that i finally figured out a method to devise fructose and would use nanobots for that and i discovered i can even use open md tool for it that its very happy that i dont have to write any simulator for this project yayy:)

right away its very happy cheerful mood since i dont know but i became really upset that my project got blocked during afternoon with thinking : ok i again came to need of writing a qm simulator :S but a less complex version, no CAD physics simulator version nor no advance thermodynamics configurations siomulations including version any. so it wouold had been a basical n body schrodinger eq. solver with also variable external parameters. so it wouldnt be like 2021's start goal project of qm simulator which would be much more complex qm simulator version since it would have been also enabling advanced theormodynamical settings outside configurations in such project e.g. turbines/flows etc etc.  so even this time the qm simulator's requirements were quite alot lesser complex, it were still very alot of effort. so i were very unhappy in afternoon's last hours thinking my project idea of composing fructose with molecular factories got blocked since i would had to write a qm simmualtor in advance. even non complex versionwould take at least a month or more effort. so i really became very upset snice this project initially seemed very practivcal type project that i wouldnt needing to spend a lot time to design phase but just easily proceed to the implementation phase.

so its very cheerful right now since i could directly swtch to implementation pahse in this first nanobots generative design task, i mean design of nanobots with generative design task, then later with such nanobots molecular factory units would be constructed to compose for instance glucose. and its so happy that i dont have to write a simulator for this since i guess openmm would suffice. 

yayyyy :) finally i have a practical side/hobby project which does not includes lots of studying time theoretical topics studying time. finally a practical hobby project to build in short period. yayyy. very happy. 

lets find out a cloud solution to be able to start designing the placement of the simulator of openmm and the nanobots generation generative design framework. 

yayyyyyyyyyy its so happy :) i finally have a practical proejct that doesn not require me to code a simulator product any and simulator product is already ready :) 

only i need to design some algorithms to capture knowledge among entropy and to capture specific modes of motion of atoms molecules to capture their cyclic motions or noncyclic momtions. so this latter part could be in tandem investigated, but first even just knowledge info might suffice to construct a generative design and be able to assess the design's right away result whether if its holding some patterns or not. 

yayyy :) i am very happy right away. for the first time for a very long time, i for the hobby projects side, i have a project that is practical to implement that i dont need to study endless theoretical study period that i would see some results directly instead of coder ai that needs alot of theoretical study in advance.

i want to celebrate this moment of adding such side project to my days :) finally a practical to implement project type that does not needs endless theoretical studying:) not endless, coder ai is also progressing, but anything in that project is slow i mean to come to even coding phasde in coder ai project for instance right away depends on finishing at least 2 phd textbooks one i am already studying and other needs to be finished. so it has endless such theoretical studying tasks that in the end you never produce any deliverable that works in cloud or pc but just iterate on the theoretical side but that is also happening very slow. and so it felt sometimes very overwhelming in coder ai project that it takes a lot time and effort to even come to coding phase/design conclusion phase. 

so its right away very cheerful to me since i finally found a practical to implement project :)

hmm lets select the cheapest spot vm instances having cloud option for this new side project (which would progress in tandem to coder ai project) : is generative design of nanobots using openmm software and trying to build some molecular factory units with nanobots like that  and to be able to design polymers or fructose/cellulose/glucose like that :) 

yayyy :)

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its very cheerful right away :)

 

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i cant believe i just can right away switch to coding directly in a side hobby project. (as you know i couldnt switch to coding in coder ai project even still, i need to finish 2 phd textbooks. it feels like never ends but of course some iterating in theoretical studies in coder ai project, but its very challenging project and very challenges me every single moment of coder ai project's building period is very very very challenging,   i just cant imagine i found a lesser challening project type as a second side project, its very happy:) in this project, unlike other project, i can just directly right away start coding :) 

wov :) maybe a dozen of papers i might read to devise some information capture methods but other than that that is very neglieable effort to me wtih respect to load of theoretical effort coder ai includes.

coder ai is a theoretically very heavy loaded proejct to impelmetn to me since i dont have phd in maths any nor had any msc nor bsc either. so the load of theoretical studies in that project felt like endless studies and hadnt ended yet. still at least need to finish very well understand study 2  phd /msc textbooks.  it felt a quite huge chalklenge its theroetical challenge's load effort load were very heavy actually but also i am surely very willing to invest that effort surely to both having phd level maths knowledge and to be abel to investigate that ideas of generative maths sides i wonder or have a coder ai product that i could delegate lots of tasks including studying textbooks and to invent with it later as mentioned before. actually i wont be the inventor of the  products either, coder ai would invent. so such project's theoretical challenges are very heavy to me since i dont hold neither bsc nor msc nor phd in maths as visible. but nevertheless i were very dedicatedy studying to that project.  no matter how much challenging it were to me. 

so right away, finding a project type that is trivial (wtr to coder ai project at least :) ) that i could right away switch to coding, a project that is practical to implement, it feels very cheerful add on project right away. i want to celebrate this moment of adding a second hobby project but this time its practical. not needing to finish phd textbooks for this project:) maybe just only dozen  papers or so or more but not any much theoretical topics to read/study this time. so it feels awesome to have at least one practical project a while in hobby side projects context

hmm now that i have two side projects: one coder ai, one generative design approaches for nanobots design project, it feels much more diverse activities instead of constant theoretical studies necessitated by the coder ai project. 

hmm so lets how do spare my evening today: i think i would spare 1 or 2 hours to nanobots project, lets call it some title like coder ai project, hmm, generated nanobots? nope. i think i would need to find a title to this seocnd project alike coder ai project. but i didnt liked generated nanobots.  hmm maybe "mol engineering is fun" project title might be ok. in short i couold call it mol engineering project. yupp. liked this project title.. i think mol engineering is ok/cool new project title. yuppp :) my new side project :) mol engineering is fun titled project:) or could be titled other funnier project titles: this time practical project :D or a practical project. nope i think mol engineering is fun is nice project title. yuppp. 

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ok some practical tasks time. maybe selection of cloud tech or reading more finishing manual of openmm software. maybe i might utilize some parallel computing framework other than mpi when utilizing it. yupp or mght follow mpi methodology either. dont know. yayyy some such practical project design decisions to be made. finally some project that is practical, e.g. selection of mpi technology named practice.  yayyyy :)

i want to celebrate this moment of such side project addition with some nice tea. or coffee. yuppp.

its very cheerful moment right away :)

back to manual reading of openMm named software yayyy :)

ok 2 hours to openmm today than would add some coder ai topology study continuation

yayy finally a more diverse study topics. some practivcal topics like openmm manual learning and cloud selection ideas and mpi technology selection etc, plus later back to coder ai project. a diverse evening study period unlike previous days which were always theoretical topics studying i mean current is topology topic related. 

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its very happy right away that i have found an interesting second project to build in tandem to coder ai project's endless studies :)

its very happy right away :) 

hmm might even create some product with this molecular factories product or nanobots based factories e.g. to devise cellulose/fructose so that we can generate salad without having have to plant a salad. that in space ships we could just print salad leaf with such molecular factory or food printer. 

but its right away just an idea, until implemented. but this time very short testing the idea period, i can right away switch to implementation this time :)

yayyy:) its so happy to have found a second software project to add to after work studies and weekedn studies :)  

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yayyy :)