Creating Volume Mesh

There are plenty of free source codes that can create a volume mesh from an STL file. But all of them can do a good job if your surface mesh is healthy without errors such as self-intersecting faces. Here, I'll use Gmsh to create a volume mesh from STL file of cleaned/repaired mesh as explained before in the previous blog entry. Gmsh can crash a lot, but don't blame the software, it's your faulty surface mesh if that happens.

Last change: April 13, 2016

Cleaning/Repairing Surface Mesh

Even though all of this is easily googlable there are countless of options and ways one can pursue to clean their STL file to be later 3D printed or used to create volume mesh for finite element calculations. This is first from the series of blog entries where I'll explain my way of creating and preparing volume meshes. It's easy to create them with plenty of open source codes, but a beginner will likely end up with too high number of elements.

Last change: April 13, 2016

Earthquake, Tsunami, Nuclear Power Plant

As it happened, I've been in the office in Tokyo when the big earthquake happened on Friday, March 11. From the intercom of the institute where I worked, we've got a warning like 10 seconds before, that it was coming. Now, that's really impressive. My colleague made a joke, he jumped under the table and we laughed.

Date: March 17, 2011

Sword Fight

I used to tell people, who saw my scar, that I had been in a sword fight. For some reason they didn't believe me. So eventually I did tell them the truth, I had fallen from my bicycle riding it to work. Well, sword fight just sounded cooler to me. It happened when taking a different route than usual...

Date: October 19, 2010

Making of Mochi (餅)

Was passing around some people cooking something funny on the street. The first two groups were looking at me like they wanted to offer me some, but I was riding my bicycle and they didn't say anything, just smiled at me politely. Later that day I met third group and this time they flagged me down and offered me their Mochi.

Date: March 30, 2010

Tokyo Dome City Roller Coaster

I live in Bunkyo-ku not far from a baseball stadium and a Tokyo Dome City with a department store, a spa and several fun attractions. One of them is a big roller coaster. I wanted to ride it the first time I saw it, but I didn't feel like doing it alone. Today I finally got the chance to go there with a friend Hideyuki.

Date: June 13, 2009

Two months in Japan and I managed to get to a hospital

I was running down the stairs, looking forward to eating the marshmallows that I wanted to buy. While running down I even told myself that once I end up with sprained ankle. I did all five floors and I slipped on the very last stair, fell down and while falling I heard a cracking noise in my ankle.

Date: June 10, 2009

How I had to steal a boat

The weather didn't look that good at first, but then they forecast cloudy only. So I woke up on Saturday morning at 5 am to catch the 6 am train to Miura-shi 73 km from Tokyo. Everyone in the train was asleep. I tried it too, but couldn't fall asleep again, Japanese seem to have mastered sleeping in public transportations.

Date: May 22, 2009

Shinjuku skyscrapers and a cemetery on my way home

My aunt's husband likes skyscrapers and she asked me to photograph some for him. So I have googled a little and discovered the Nishi-Shinjuku skyscraper business district in Tokyo. I bicycled to the subway station in my area, locked the bike outside and rode the train to the Nishi-Shinjuku subway station.

Date: May 10, 2009

Wakasu Island

I got off of the subway at some place that on the map looked close enough to some water. I didn't know which direction to go, but, somehow intuitively, after few minutes of walking I managed to feel the familiar smell of the ocean. When I left Portugal around one year ago I tried to convince myself that I wouldn't miss it.

Date: May 02, 2009


I sat on my bicycle in the morning with the intention of just having a wander around, just aimlessly pedaling among the pedestrians and discovering the city. After a few minutes I was happy about how good I was at zigzagging between the people. I went only as far as to feel at least a little confident about my being able to return.

Date: April 29, 2009


I left the hotel in Paris at 6:30 am after 5 hours of sleep. Too early, I thought, the flight was scheduled on 11:50 am. At the train station, they changed the platform from where the train to the airport was running. There they informed us that the train didn't go all the way to the airport and that we had to take a bus from certain station.

Date: April 18, 2009

The last weekend in France

The weather was cold, cloudy with drizzle when I arrived to Vannes on Saturday. I checked in at my hotel and went out to explore the city. During the afternoon I crisscrossed the whole city center twice. Although I enjoyed the walk along the river, I decided to check if it was possible to change my train ticket for earlier departure on Sunday.

Date: April 6, 2009

Looking for a Post-Doc all around the globe

So far, I have been going twice through the process of looking for a Post-Doc position. Although I have been mostly focused on the world of biomechanics, some of the links provided here are useful in general for the field of your choice. If you know about any other useful link of this kind, please, leave a comment.

Last change: April 7, 2009

Paris vs. Lisbon

I realize that comparing two cities like that is not correct. I could be accused of generalizing. But of course there are always some exceptions to everything, that goes without saying. I am going to talk about the average people and situations. Although, in my five years and seven months in Lisbon, the city has changed.

Date: February 24, 2009


One of my trips, related to my current project, was to Germany. I was to see an accident analyst and study some real accident scenarios involving motorcyclists. Mostly sad stuff. It's amazing that in most of the cases the helmet gets off of the head during the accident.

Date: February 14, 2009

My stolen underwear

I have a routine I do every single day. I wake up, walk to the mirror to check if I am still handsome, go to the bathroom to take a whiz, return back to the room, take the shorts off, throw them on the bed next to the pillow and put on the proper underwear and jeans.

Date: January 21, 2009

Les Calanques de Marseille

I went to the Gare du Nord station, although I was supposed to be at the Gare de Lyon station. But I couldn't find it on the map, so I thought that Gare du Nord must be enough. They have explained to me there that I still have to go two more stations by the RER train, to get to Gare de Lyon. So, now I know where on the map it is.

Date: September 24, 2008


Altair's French office 'Altair Development France' has helped to develop a detailed finite element model of an entire human body. Basicaly a human body was frozen in a car driving position, cut into thin slices from which the geometry was exctracted to create the computational model called HUMOS, version 2 by now.

Date: September 17, 2008

Emergency call

I had a heatstroke with fever of nearly 40 °C (104 °F). When it reached this level at two o'clock in the morning, I decided to dial european emergency number 112. Since body temperatures above 40 are life-threatening, I just didn't want to risk the fever to rise any more, at 41 °C (106 °F) brain death begins.

Date: August 8, 2008

MYMOSA project

From May 5, 2008 I am a part of the MYMOSA (MotorcYcle and MOtorcyclist SAfety) project. As its official web page says: ‘MYMOSA is a Research Training Network composed of a well-balanced group of 5 universities, 3 research centres and 6 companies.’

Date: Jun 9, 2008

Saying Goodbye to the Cliffs

My days in Portugal are numbered and therefore I wanted to give goodbye to the cliffs where I and my friend Plz used to go hiking. I always thought that Czechs and Slovaks like hiking a lot, but even so it was difficult to find someone to go with me. I tried to convince more people, but only one Czech girl Jana showed the interest to join me.

Date: March 18, 2008

I had a dream

Well, naturally, I had a lot of dreams in my life and I usually didn’t talk about them, but this one was hilarious, so I had to write it down. I hope I am not the only one who finds it funny.

Date: February 15, 2008

Magical situation I have witnessed

Now, that I have more time, waiting for the defence of my thesis, I walk to my office eight kilometres in the morning and another eight back in the evening. It takes me an hour and a half to get there, but I enjoy it, thinking about many things.

Date: January 28, 2008

Slovak-Hungarian conflict (not only) on YouTube

Since I am Slovak living abroad for over five years now, in nostalgic times I feel the need to read or watch something, preferably nice, about Slovakia. For this reason I watched some, to my native country related, videos on YouTube. I have been shocked reading the comments, though.

Date: November 15, 2007

How to take care of an elderly person who fainted?

As every morning, I was on my way to the university. The bus I took was half empty. I was minding my own business reading a book, when I noticed that the movement of the people around was suddenly more intense. There was a lady who fainted. She could be over 50 years old.

Date: November 08, 2007

He told us to go away from Portugal

A very good friend of mine, who used to live in Lisbon for almost two years, came back for four days. She was very happy and excited to be back, since she still didn't get used to the real life back home. I wonder if I'm going to feel like that too. We were visiting the old good places she liked so much.

Date: March 05, 2007

On my way down from 12th floor

Saturday morning, I woke up before eight. There were three degrees Celsius outside, seven inside of my flat. I put on my warm rope and went to the bath room. There was no water coming out of the tap. I remembered when, shortly after midnight coming back home, there was a floor full of water down in front of the elevators.

Date: January 27, 2007

Bicycle touring through northern Setubal Peninsula

Although some of the people of Portugal tried to persuade me from my travel plan, I didn’t give up. Almost nobody could understand that I want to spend a weekend on bike and sleep outside under the stars. It made me a bit worried though, but at least I was more careful.

Date: March 12, 2006

Sunrise over Vasco da Gama bridge

I planned to photograph the Vasco da Gama bridge during sunrise long time ago. At last, today morning I woke up at half past four, sat on a bicycle and after forty minutes was already standing at the place under the light of a street lamp.

Date: May 03, 2005